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Rubber (Hevea brasiliensis, (Willd. Ex Adr. de Juss) Muell. Arg, Euphorbiaceae) is an important commercial latex-producing plant. Commercially, rubber is reproduced from a limited number of grifting genotypes. New promising genotypes have been selected to replace traditional genotypes. In addition, rubber has been promoted to recuperate Amazon soils degraded by extensive cattle ranching. Arbuscular mycorrhizal (AM) symbiosis is an important alternative for improving plant nutrition in rubber trees and recuperating degraded soils, but AM fungal communities on different plantations and in rubber genotypes are unknown. Spore abundance, root colonization and AM fungal community composition were evaluated in rubber roots of Colombian and introduced genotypes cultivated in degraded soils with different plantation types. Traditional (spore isolation and description; clearing and staining roots) and molecular techniques (Illumina sequencing) were used to assess AM fungi. Rubber roots hosted a diverse AM fungal community of 135 virtual taxa (VT) in 13 genera. The genus Glomus represented 66% of the total AM fungal community. Rubber genotype did not affect the arbuscular mycorrhization, hosting similar AM fungal communities. The composition of the AM fungal community on old and young rubber plantations was different. Diversity in AM fungi in rubber roots is an important characteristic for restoring degraded soils.
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Arbuscular Mycorrhization in Colombian and Introduced
Rubber (Hevea brasiliensis) Genotypes Cultivated on Degraded
Soils of the Amazon Region
Clara P. Peña-Venegas *, Armando Sterling and Tatiana K. Andrade-Ramírez
Citation: Peña-Venegas, C.P.;
Sterling, A.; Andrade-Ramírez, T.K.
Arbuscular Mycorrhization in
Colombian and Introduced Rubber
(Hevea brasiliensis) Genotypes
Cultivated on Degraded Soils of the
Amazon Region. Agriculture 2021,11,
Academic Editors:
Isabelle Trinsoutrot-Gattin
and Babacar Thioye
Received: 3 March 2021
Accepted: 26 March 2021
Published: 16 April 2021
Publisher’s Note: MDPI stays neutral
with regard to jurisdictional claims in
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Copyright: © 2021 by the authors.
Licensee MDPI, Basel, Switzerland.
This article is an open access article
distributed under the terms and
conditions of the Creative Commons
Attribution (CC BY) license (https://
Sinchi Amazonic Institute of Scientific Research, Leticia 910001, Colombia; (A.S.); (T.K.A.-R.)
*Correspondence:; Tel.: +57-3108149907
Rubber (Hevea brasiliensis, (Willd. Ex Adr. de Juss) Muell. Arg, Euphorbiaceae) is an
important commercial latex-producing plant. Commercially, rubber is reproduced from a limited
number of grifting genotypes. New promising genotypes have been selected to replace traditional
genotypes. In addition, rubber has been promoted to recuperate Amazon soils degraded by extensive
cattle ranching. Arbuscular mycorrhizal (AM) symbiosis is an important alternative for improving
plant nutrition in rubber trees and recuperating degraded soils, but AM fungal communities on
different plantations and in rubber genotypes are unknown. Spore abundance, root colonization and
AM fungal community composition were evaluated in rubber roots of Colombian and introduced
genotypes cultivated in degraded soils with different plantation types. Traditional (spore isolation
and description; clearing and staining roots) and molecular techniques (Illumina sequencing) were
used to assess AM fungi. Rubber roots hosted a diverse AM fungal community of 135 virtual taxa
(VT) in 13 genera. The genus Glomus represented 66% of the total AM fungal community. Rubber
genotype did not affect the arbuscular mycorrhization, hosting similar AM fungal communities.
The composition of the AM fungal community on old and young rubber plantations was different.
Diversity in AM fungi in rubber roots is an important characteristic for restoring degraded soils.
Keywords: Amazon; grifting plants; soil restoration
1. Introduction
Rubber (Hevea brasiliensis, (Willd. Ex Adr. de Juss) Muell. Arg, Euphorbiaceae) is a
native species from the Amazon region and an important commercial plant species. It is
cultivated in more than 40 countries for latex production [
]. Global consumption of natural
rubber is increasing. Between 2000 and 2018, rubber consumption increased 96.23% [2].
Global rubber production is based on the cultivation of a few rubber clones that are
reproduced from grifting stumps. Although it secures homogeneity in latex production,
the lack of genetic diversity increases susceptibility to phytosanitary problems and reduces
rubber latex yielding. Producers are creating new plantations in areas that were covered
by natural tropical forests [
], avoiding common diseases such as the South American leaf
blight (SALB), caused by Pseudocercospora ulei (Henn.),with negative consequences for
natural ecosystems. Others are developing new rubber genotypes with more resistance
to diseases and good latex production [
] for cultivation in traditional areas. The genetic
improvement of commercial rubber is not enough to guarantee good latex production
because cultivated plants require good nutrition. Commercial plantations require regular
fertilization during the 25-year production cycle, which increases latex production cost.
Although Asiatic countries are the main latex rubber producers, rubber is still an
important crop in Amazonian countries. In the Amazon region of Colombia, 4534 Ha
are cultivated with rubber, producing 183 tons of latex per year [
]. In Colombia, rub-
ber production is based mainly on three introduced genotypes—IAN 873, IAN 710, and
Agriculture 2021,11, 361.
Agriculture 2021,11, 361 2 of 17
FX 3864 [6]
. These rubber genotypes have been planted in areas with a high incidence of
SALB, resulting in a high presence of the disease and low local latex production [4].
In the Colombian Amazon, rubber has been promoted as a key crop recuperating
degraded areas after years of extensive cattle ranching. Therefore, around 70 Ha of rubber
trees were planted on degraded pastures with the purpose of transforming these unpro-
ductive areas into sustainable productive ones. Naturally, most of the Amazon basin has
low-fertility soils [
], in which phosphorus (P) is usually the limiting soil nutrient. De-
graded Amazon soils have very low P levels that are sometimes undetectable by traditional
P analyses (e.g., less than 0.09 mg/Kg soil by Bray II). Although rubber is a native species
from the Amazon region, it can experience P deficiencies, which manifest as lower leaf
production in young rubber trees, brown color on leaf edges, less growth, and lower latex
production in mature rubber trees [
]. Low-cost alternatives that improve soil conditions
for rubber plantations are becoming an important issue for producers.
Arbuscular mycorrhization seems to be a feasible low-cost alternative that improves
latex production locally because it occurs naturally in rubber [
]. Arbuscular mycorrhiza
is a symbiosis between plant roots and Glomeromycota obligate endosymbiont fungi [
occurring in about 80% of all plants. Arbuscular mycorrhiza is identified as the main plant–
root association in crop species that mobilizes nutrients to plants, especially P, improving
nutrition even in low fertile soils [
]. This association also reduces stress in host plants
produced by water or nutrient limitations or the presence of contaminants or pathogens [
Although it seems to be the best alternative for a more sustainable and chipper rubber tree
agriculture, there are still some unsolved issues that limit our knowledge on how grifting
plants react to arbuscular mycorrhizal associations.
Grifting plants as commercial rubber are still physiologically poorly understood.
Some authors consider them as individual plants that interact, while others consider them
as hybrid plants with unique and individual autonomy [
]. The latter is based on the
observed root-top relationship of grafting plants, in which upward water and mineral
nutrient supply, downward flow of photosynthates, and root-top interchange of hormonal
signals change [
]. Symbiotic associations such as arbuscular mycorrhiza might offer
insights into how gifting plants behave. If grifting plants act as different individuals
downward and upward, arbuscular mycorrhizal (AM) associations will not be affected by
upward genotypic variations. However, if grifting plants act as hybrids, upward genotypic
variations will affect root affinity by AM fungi and therefore AM associations among
different clones.
Ecologically, plants with a high affinity for arbuscular mycorrhizal (AM) fungi ben-
efit themselves and the plant community around them [
]. Therefore, AM symbiosis
might play an important role in recovering degraded soils [
]. Different results support
or deny the importance of rubber as an AM host plant in the restoration of environ-
ments. Based on soil spore-borne AM fungi, Feldmann et al. [
] found higher AM fungal
diversity in natural rubber stands than in commercial monoclonal plantations. These
differences were attributed to crop management practices on rubber plantations. How-
Herrmann et al. [9]
found highly diverse communities of AM fungi on commercial
plantations of rubber cultivated in Thailand despite the high levels of applied fertilizers.
Since arbuscular mycorrhiza occurs at the root level, it is not well understood whether
genomic variation or environmental and abiotic factors affect more AM symbiosis in rubber.
Rubber production in the Amazon region offers a good environment for addressing these
issues. Since 2009, the Sinchi Institute has selected promising introduced and Colombian
rubber genotypes that are less susceptible to common pathogens and have good potential
for latex production [
]. Sterling and Rodriguez [
] compared plant growth, resistance to
phytopathogens, and potential latex production between promising rubber genotypes and
the introduced genotype IAN 873 (control) indicating that new genotypes performed better
than IAN 873. For a better understanding of arbuscular mycorrhizal association in rubber,
this study (i) established differences in the AM fungal community associated with rubber
roots cultivated on different plantation types, (ii) determined the influence of soil variables
Agriculture 2021,11, 361 3 of 17
on the AM fungal community associated with these rubber plantations, and (iii) evaluated
the root colonization and AM fungal community composition of Colombian and introduced
rubber genotypes cultivated in degraded soils of the Colombian Amazon region.
2. Materials and Methods
2.1. Sites and Samples
Samples were collected in five municipalities of the Caquetástate, Colombian Amazon
region: Albania, Belen de los Andaquíes, Florencia, El Paujil, and San Vicente del Caguán.
The study area was located at 1
15” N to 02
41” N, and 74
39” W to 75
2” W
(Figure 1). The elevation in this area ranges between 245 and 559 m above sea level. The
average annual rainfall is around 3000 mm, with a dryer period between December and
February. The average annual temperature is up to 24
C [
]. The area corresponded to
the upper Amazon basin and is influenced by the Andes mountain chain. Soils in the study
area are classified as Inceptisols and Oxisols (USDA soil classification). The area is covered
by introduced pastures for extensive cattle ranching with different levels of degradation,
commercial rubber plantations, and some relicts of natural secondary forests.
Figure 1. Map with the location of the study area. Scale: 1:2,000,000.
Four types of rubber plantations were visited to collect soil and root samples—three
monoclonal plantations (MPs) between 30 and 50 years old with introduced rubber geno-
types; two six-year-old agroforestry systems (ASs) in which introduced genotypes of rubber
were intercropped with copoazu fruit trees (Theobroma grandiflomum (Willd.
Ex Spreng.
K.Schum.); three nine-year-old clonal trials with introduced genotypes (CTIGs); and three
one-year-old clonal trials with Colombian rubber genotypes (CTCGs), plus the intro-
duced genotype IAN 873 (traditional cultivar) as a control for comparisons (Table S1,
Supplementary Materials).
Rubber plantations differed in their agronomic management. MPs were cleaned pe-
riodically of weeds and fertilized once per year with an inorganic NPK fertilizer. ASs
received weed control every three months and fertilization twice per year with organic fer-
tilizers. Additionally, two commercial insecticides were applied every 15 days to copoazu
trees when insects were causing phytosanitary problems [
]. CTCGs and CTIGs received
weed control every three months and fertilization with a mix of organic and inorganic
fertilizers every six months. Phytosanitary controls were not performed on the latter two
plantation types [22].
Agriculture 2021,11, 361 4 of 17
On each plantation, two types of samples were collected—soil samples and rubber
tree root samples. A composed topsoil sample of about 500 g from 5 sub-samples of 100 g
was collected to evaluate (i) the physicochemical composition of the soils where rubber
tree was growing, (ii) the relative abundance of soil-borne AM fungal spores, and (iii) the
AM fungal community composition at the family level. Soil samples were dried at room
temperature to reduce the percentage of humidity and transported to the laboratory in
plastic bags.
Root samples were used to estimate (i) the percentage of AM root colonization and
(ii) the
AM fungal community composition of rubber roots. Between 5 to 15 fine root
samples of individual rubber trees were collected in each site from the bulky roots present
in the first 20 cm of soil depth. The length of fine roots collected from each plant ranged
between 3 and 10 cm approximately. A total of 255 root samples were collected. Root
samples were transported in paper bags to the laboratory where root samples were divided
in two: one-half of each sample was fixed in a Formalin-alcohol solution (Formaldehyde-
ethanol-water 1:1:2) to estimate the percentage of AM root colonization. From the second
half, a subset of 160 samples was stored at
C and used to estimate the AM fungal
community composition with molecular approaches. The subset included root samples of
at least one replicate of each plantation type, with root samples of all rubber tree genotypes.
The number of soil and root samples that were collected and analyzed is summarized
in Table S1, Supplementary Materials.
2.2. Soil Physicochemical Analysis
Soil samples were processed to estimate the following soil physicochemical properties:
soil texture (Bouyoucos); pH (1:1 in water); percentage of organic carbon (with potassium
dichromate solution); cation exchange capacity (CEC), Ca, Mg, K, and Na expressed in
mg/kg of dry soil (with 1N ammonium acetate at pH = 7); and available phosphorus (P)
expressed as mg/kg of dry soil (Bray II).
2.3. Extraction of AM Spores from Field Soils
About 25 g of each soil sample was used to extract AM fungal spores present in
each soil. Five replicates of each soil sample were processed. Spores were obtained by
wet sieving, followed by centrifugation in a saturated sucrose solution [
]. Isolated
soil-borne AM fungal spores were placed in Petri dishes and counted directly with a stere-
oscope (
SZ40 Olympus
, Allentown, PA, USA). Distinctive AM fungal spore morphotypes
were mounted on slides with lactoglycerol (LG) (Lactic acid: Glycerol: water 1:2:1) and
LG + Melzer’s
reagent (Micro-science, London, UK) (1:1 v/v) and observed under a com-
pound microscope (BX53 Olympus, Allentown, PA, USA) in order to classify the spores
into particular AM fungal families.
2.4. AM Fungal Colonization of Rubber Roots
Root samples were processed by clearing and staining roots with a solution of 0.05%
trypan blue in lactoglycerol [
]. The percentage of AM root colonization was estimated by
the gridline intersect method [
], obtaining the total percentage of AM root colonization
in 100 root intersections. The procedure was repeated thrice per sample.
2.5. Molecular Analysis of Rubber Roots
DNA was obtained from 0.2 g of dried roots using the PowerMax
Soil DNA Isola-
tion Kit (Qiagen, Germantown, MD, USA). This DNA was quantified with Nanodrop
Thermo Fisher Scientific
, Madison, WI, USA) before sequencing. The AM fungal DNA
was amplified from samples using AM fungal specific primers for the small-subunit (SSU)
ribosomal RNA gene—WANDA [
] and AML2 [
]. The PCR mixture contained 5
L of
5XHOT FirePol Blend Master Mix (Solis Biodyne, Tartu, Estonia); 0.5
L of each 20
primer; 1
L of template DNA; and nuclease-free water to reach a total reaction volume
of 25
L. The PCR was performed following the thermocycling conditions reported by
Agriculture 2021,11, 361 5 of 17
Davison et al. [
]: 95
C for 15 min, 30 cycles of 95
C for 30 s, 55
C for 30 s, and 72
for 30 s, followed by 72
C for 5 min. PCR products and the amplification success were
checked on 1% agarose gel. Both negative (distilled water) and positive (synthetic double-
stranded DNA with relevant priming sites) controls were included in the PCR to secure
the quality of the PCR products. A DNA concentration of 5 ng/
L was used for the library
preparation. A library was prepared for each sample. The library preparation was carried
outusing a modified Illumina 16S rRNA protocol, standardized by Asper Biogene. Each
library was ligated with Illumina adaptors using the TruSeq DNA PCR-free library prep kit
Illumina Inc.
, San Diego, CA, USA). The second PCR used a reaction mix composed of
of PCR product of fist PCR, 5
L of Nextera XT index 1 primer (N7xxx), 5
L of Nextera XT
index 2 primer (E5xxx), and 15
L of 2
KAPA HiFi Hotstart PCR mix (without KAPA
primer). The PCR program was run as follows: 3 min at 95
C, followed by 7 cycles of 30 s
at 95
C, 30 s at 55
C, and 30 s at 72
C, with a final extension of 5 min at
72 C
and held at
C. Libraries were sequenced on the Illumina MiSeq platform (
Illumina Inc.,
San Diego,
CA, USA) using a 2
300 bp paired-read sequencing approach at Asper Biogene laboratory
(Tartu, Estonia). A total of 22,810,852 raw sequences and 17,632,788 clean sequences were
obtained, which corresponded to 77.3% of the total sequences. The raw sequences are
available under request.
2.6. Bioinformatics
Demultiplexed paired-end reads were analyzed according to the bioinformatics steps
described by Vasar et al. [
]. Primer sequences were matched allowing one mismatch
in forward or reverse chains. Removal of barcode and primer sequences was conducted
using the PEAR v. 0.9.8. program. Singletons were removed, and amplicons between
170 and 540 pb
in length were included in the analysis. Amplicons longer than 540 bp
were cut at that length and conserved for further analysis. Chimeric sequences were de-
tected and removed using UCHIME v7.0.1090 [
] in the reference database mode using
the default parameters and MaarjAM database (, accessed
8 January 2021
, status June 2019, 384 virtual taxa (VT)). Sequence alignment was per-
formed using the MAFFT v. 7 multiple sequence alignment web service in JALVIEW
version 2.8 [31]
, subjected to a neighbor-joining phylogenetic analysis in TOPALi v2.5 [
using the default parameters with the MaarjAM and the International Nucleotide Sequence
Database Collaboration (INSDC). Retained reads were subjected to a BLAST+ search
v 2.8.1 [33]
using 97% identity and 95% alignment length thresholds. Representative se-
quences of Glomeromycota virtual taxa (VT) were deposited in the NCBI GenBank under
the accession numbers (MW900266 to MW900422).
2.7. Statistical Analysis
Differences in the abundance of soil-borne spores and in the percentage of AM root
colonization among the plantation types were assessed using linear mixed-effects mod-
els (LMEs) (plantation identity as a random effect) (function lme from the R package
v. 3.5.1. nlme
). When significant differences were obtained, a Tukey honest significant
difference (HSD) test was performed with a p< 0.05 value to discriminate significant
differences. Additionally, comparisons in the percentage of root colonization and richness
between the Colombian and introduced rubber tree genotypes within the same plantation
type were assessed using a Kruskal-Wallis test from the R program v. 3.5.1.
Sampling efficacy was assessed with species accumulation curves (method “exact”)
using the functions accumcomp and ggplot from the R packages BiodiversityR and ggplot2,
respectively [
]. The AM fungal richness between the plantation types and between
the genotype types was visualized with Venn diagrams using the function ggvenn from R
package ggven [
]. The AM fungal richness (S) and diversity indices (Shannon-Wiener,
InvSimpson, and Pielou’s evenness) were estimated using the functions Specnumber and
diversity from the R package vegan [
]. The Shannon index (H’) was exponentially
transformed to obtain a variable (expH’) that satisfied the replication principle, following
Agriculture 2021,11, 361 6 of 17
Herrmann et al. [
] recommendations. An LME (function lme from the R package nlme) [
was adjusted to analyze the effect of the plantation type or genotype type on ecological
indices. The effect of the plot (plantation identity or genotype identity) was included as a
random effect in each model for the nested study design. The differences in mean variables
among the plantation types or between the genotype types were analyzed with the Fisher’s
least significant difference LSD post hoc test (α= 0.05).
A nested permitational multivariate analysis of variance PERMANOVA using the
function nested.npmanova from the R package BiodiversityR [
] was performed to compare
the AM fungal community composition among the plantations and between the genotypes.
A non-metric multidimensional scaling ((NMDS), 50 iterations) was used (Bray-Curtis
distance) and plotted with two axes and standard deviations ellipses (
= 0.05) to visualize
changes in the AM fungal community composition among the plantation types. The
functions metaMDS and ordiellipse (R package vegan), and ggplot and theme (R package
ggplot2) were used [
]. The indicator species value analysis was used to study the
strength of the relationship between the AM fungal VT and the rubber plantations or the
AM fungal VT and the rubber genotypes (function indval from the R package labdsv [
An indicator value species of at least 0.25 was considered as a good indicator taxon [9].
Soil physicochemical variables were analyzed with LME and the means pairs were
compared with Fisher’s LSD post hoc test (
= 0.05). Spearman’s correlation was used
to relate the AM fungal diversity with the soil variables. The AM fungal community
composition data were Hellinger transformed and included with all soil variables in a
redundancy analysis (RDA) in order to assess the effect of soil variables on the AM fungal
community composition (function rda from the R package vegan) [
]. Sequential ANOVA
tests (1000 iterations) were performed for the contribution of each soil variable. The
importance of individual AM fungal VT was determined using the parameter r
α= 0.05
) to better explain the variation among the plantation types. RDA was plotted with
two axes in a triplot graphic using functions ordiellipse and envfit (R package vegan) [
and ggplot and theme (R package ggplot2) [35].
The analyzes were performed in R language, v. 4.0.3 [
] using the interface in
InfoStat v. 2020 [
] for the LME, Fisher’s LSD, and Spearman’s tests; the interface in Qeco
v. 2018 [42]
for the formal ecological analyses; and the interface in RStudio v. 1.3.1093 [
for the graphical analyses.
3. Results
3.1. Soil Conditions of Rubber Plantations
Soil physicochemical analysis indicated that the soils where the rubber was cultivated
had nutritional limitations. The available P was one of the most limited soil nutrients for
plant growth, with values lower than 2 mg/kg of soil (Table 1). There was a significant
difference in the content of sodium among the plantation types. AS and MP had more
sodium than CTCG and CTIG.
Table 1.
Soil physicochemical composition of the rubber tree plantations: clonal trial with Colombian genotypes (CTCG);
clonal trial with introduced genotypes (CTIG); agroforestry system (AS); and monoclonal plantation (MP).
Plantation Type SOIL Physicochemical Variables
pH OC (%) CEC
(meq/100g) Loam (%) Clay (%) Sand (%)
CTCG 4.62 ±0.04a 1.37 ±0.24a 10.46 ±1.62a 14.14 ±0.46a 47.77 ±3.55a 38.71 ±4.03a
CTIG 4.62 ±0.05a 0.85 ±0.29a 7.05 ±1.67a 8.14 ±0.66b 43.33 ±4.38a 48.33 ±4.86a
AS 4.55 ±0.08a 1.17 ±0.29a 5.94 ±1.65a 13.98 ±0.35a 49.00 ±5.36a 40.71 ±4.99a
MP 4.55 ±0.05a 1.15 ±0.24a 7.13 ±1.54a 8.00 ±0.00b 49.33 ±4.37a 42.67 ±3.94a
K (mg/kg) Ca (mg/kg) Mg (mg/kg) Na (mg/kg) P (mg/kg)
CTCG 67.48 ±8.37a 330.45 ±30.47a 58.90 ±6.58a 32.79 ±3.26b 1.31 ±0.46a
CTIG 40.13 ±10.41a 212.29 ±34.99a 35.99 ±7.72a 29.64 ±4.03b 0.59 ±0.58a
AS 38.60 ±9.78a 255.18 ±40.88a 46.00 ±7.55a 46.03 ±4.00a 1.09 ±0.55a
MP 55.51 ±9.13a 238.00 ±27.78a 32.67 ±6.16a 49.32 ±3.96a 0.73 ±0.45a
OC: organic carbon, CEC: cation exchange capacity, K: potassium, Ca: calcium, Mg: magnesium, Na: sodium, and P: available phosphorus.
Values in columns corresponded to mean and standard error. Values followed by the same letter do not differ statistically (Fisher’s least
significant difference LSD test, p< 0.05).
Agriculture 2021,11, 361 7 of 17
3.2. Abundance of Arbuscular Mycorrhizal Spores in Soils
Significant differences in the abundance of AM fungal spores were found among the
rubber plantations (p= 0.001). Spore abundance in MP was significantly lower than in AS
and CTIG (Figure 2).
Figure 2.
Spore abundance of arbuscular mycorrhizal fungi in soils on different rubber tree planta-
tions: AS: agroforestry; MP: monoclonal plantation; CTIG: clonal trial with introduced genotypes;
and CTCG: clonal trial with Colombian genotypes. Spore abundance expressed as the number of
spores per 100 g of dry soil. Letters express significant differences.
3.3. Arbuscular Mycorrhizal Fungal Colonization of Rubber Roots
All rubber root samples were colonized by AM fungi, with percentages of colonization
between 1 and 96%. There were significant differences in the percentage of AM root colo-
nization among the different rubber plantations (p < 0.0001). MP and AS had significantly
higher percentages of AM root colonization (66
17% and 57
23%, respectively,
Figure 3
than the clonal trials. Root colonization on the other rubber plantations was between 36
and 47% on average.
Figure 3.
Percentage of arbuscular mycorrhizal colonization of rubber roots cultivated on dif-
ferent plantation types: clonal trial with Colombian genotypes (CTCG); clonal trial with intro-
duced genotypes (CTIG); monoclonal plantation (MP); and agroforestry system (AS). Letters express
significant differences.
Agriculture 2021,11, 361 8 of 17
There were no significant differences in the percentage of AM root colonization be-
tween the Colombian (46%) and introduced (44%) rubber genotypes (p= 0.665), even when
Colombian and IAN 873 were growing on the same plantation (p= 0.368;
3.4. Arbuscular Mycorrhizal Fungal Community in Rubber Roots
Accumulation curves of VT in rubber roots cultivated on different plantations indi-
cated that AM fungal community composition on CTCG was properly estimated but not
on the other rubber tree plantations (Figure 4). According to the Chao index, 95% of the
total AM fungal community colonizing rubber tree roots in CTCG was estimated, 85% in
CTIG, 84% in MP, and 81% in AS.
Figure 4.
Accumulation curves of the virtual taxa colonizing rubber root samples collected on
different types of plantations: clonal trial with Colombian genotypes (CTCG); clonal trial with
introduced genotypes (CTIG); agroforestry system (AS); and monoclonal plantation (MP).
Glomeraceae represented more than 77% of the total AM fungal community associated
with rubber tree roots independent of the approach used to estimate the AM fungal
community composition. However, the molecular approach increased the number of
VT of the families Archaeosporacee and Gigasporaceae, compared to the soil-born spore
approach (Figure 5).
The sequencing approach estimated a total of 419,089 Glomeromycotina sequences.
Sequences corresponded to 135 VT of 13 genera. Rubber plantations were highly diverse,
with more than seven different AM fungal genera per plantation. Glomus with 89 VT was
the most diverse and the most frequent genus, representing 66% of the total AM fungal
community in rubber roots. Three additional important genera colonizing rubber roots
were Acaulospora with 10 VT, Paraglomus with nine VT, and Archaeospora with eight VT,
representing 20% of the total AM fungal community. Other AM fungal genera in rubber
roots, with less frequency, were Claroideoglomus and Scutellospora with five VT, Rhizophagus
with three VT, and Ambispora,Diversispora, Gigaspora, Kuklospora, Redeckera, and Viscospora,
Agriculture 2021,11, 361 9 of 17
with one VT each. On average, each rubber plantation and each rubber root sample hosted
22 and 23 VT, respectively. The complete list of VT obtained in this study is summarized in
Table S2, Supplementary Materials.
Figure 5.
Community composition of arbuscular mycorrhizal fungi associated with rubber roots
cultivated on different types of plantations: clonal trial with Colombian genotypes (CTCG); clonal
trial with introduced genotypes (CTIG); monoclonal plantation (MP); and agroforestry system (AS).
Community composition was estimated by two different methodologies—soil spore-borne approach
and sequencing approach.
The PERMANOVA analysis showed significant differences between the AM fungal
community composition associated with different rubber plantations (p= 0.027) (
Table 2
but did not in those colonizing different rubber genotypes (p= 0.068). The NMDS plot
separated the AM fungal communities of MP from AS, CTIC, and CTCG (Figure 6). In
addition, the AM fungal communities of AS were separated according to the location of
the AS.
Table 2. Characteristics of rubber plantations and their arbuscular mycorrhizal (AM) fungal composition.
Type Rubber Tree Genotypes Plantation Identity Age (Years) Geographic Location Number
Samples aTotalNumber of AM
Fungal Reads
Number of
Vitual Taxa
Promising Colombian genotypes: ECC 25, ECC 29, ECC 35,
ECC 60, ECC 64, ECC 66, ECC 73, ECC 83, ECC 90 and IAN 873
(traditional cultivar)
CTCG 1 1 El Paujil 10 37,631 53
CTCG 2 1 San Vicente del Caguán 10 32,814 80
Promising Colombian genotypes (in a continuous sequence):
ECC 101 to ECC 199, and IAN 873 (traditional cultivar). The
genotype ECC 169 had not samples for molecular analysis
CTCG 3 1 El Paujil 99 140,362 99
Promising introduced genotypes: CDC 312, CDC 56, FDR 4575,
FDR 5597, FDR 5788, FX 3899 P1, FX 4098, GU 198 and MDF
180, and IAN 873 (traditional cultivar)
CTIG 1 9 Florencia 10 40,249 78
CTIG 2 9 San Vicente del Caguán 10 26,622 78
AS Promising introduced genotypes: FX 4098 and FDR 5788, and
IAN 873 (traditional cultivar)
AS 1 6 Albania 4 30,670 44
AS 2 6 San Vicente del Caguán 4 4784 35
MP Introduced genotypes planted as traditional cultivars: FX 3864,
FX 25 or IAN 873
MP 1 30 San Vicente del Caguán 4 36,188 32
MP 2 50 Belén de los Andaquíes 4 25,226 44
MP 3 50 Florencia 4 44,543 50
CTCG: clonal trial with Colombian genotypes; CTIG: clonal trial with introduced genotypes; AS: agroforestry system; MP: monoclonal
plantation. aOne representative sample for each genotype was obtained.
Agriculture 2021,11, 361 10 of 17
Figure 6.
Non-metric multidimensional scaling (NMDS) plots displaying AM fungal communities colonizing rubber roots.
Ellipses indicate one standard deviation around the centroid position of each rubber plantation.
The most abundant VT colonizing rubber roots was Paraglomus VT444, with
50,279 reads
Some VT were identified as indicator species of plantation types or rubber tree genotypes
(Table S3, Supplementary Materials). Most of the indicator species identified were
(82% of all indicator species), Acaulospora and Archaeospora (each representing 5% of all in-
dicator species), Gigaspora, and Scutellospora (each representing 2% of all indicator species).
3.5. Richness and Diversity of Arbuscular Mycorrhizal Fungal in Rubber Roots
Around 27% of the total VT was shared among all rubber tree plantations. Only CTCG
showed a high number of exclusive VT (around 19%), while the other plantation types
had less than 5% of exclusive VT (Figure 7a). The AM fungal community compositions in
roots of Colombian and introduced rubber genotypes were very similar. The Colombian
and introduced rubber genotypes shared around 70% of the total AM fungal community
(Figure 7b).
VT richness colonizing rubber roots was significantly different among the plantation
types (p < 0.001) but not between the rubber tree genotypes (p= 0.665), even if they
(Colombian vs. IAN 873) were growing on the same plantation (p= 0.429). CTIG and MP
hosted significantly more AM fungal VT than the other plantation types (Table 3). Only the
exponential Shannon index showed significant differences in the diversity of the different
rubber plantations (Table 3).
Agriculture 2021,11, 361 11 of 17
Figure 7.
Arbuscular mycorrhizal fungal community colonizing rubber roots in (
) different plantation types (CTCG: clonal
trial with Colombian genotypes; MP: monoclonal plantation; AS: agroforestry system; CTIG: clonal trial with introduced
genotypes) and (b) between Colombian and Introduced rubber genotypes.
Table 3.
Richness and diversity indexes of AM fungal colonizing roots of Colombian and introduced rubber genotypes and
different plantation types: CTCG (clonal trial with Colombian genotypes); CTIG (clonal trial with introduced genotypes);
AS (agroforestry system); and MP (monoclonal plantation).
Factor Level Richness (S) Exponential
Shannon (expH0)
Inverse Simpson
1/D Evenness (Piélou)
Genotype type Colombian 20.75 ±2.78a 5.26 ±0.73a 3.68 ±0.40a 0.53 ±0.03a
Introduced 25.08 ±1.88a 6.85 ±0.55a 4.67 ±0.35a 0.58 ±0.02a
Plantation type
CTCG 20.80 ±2.04b 5.42 ±0.44b 3.82 ±0.22a 0.53 ±0.02a
CTIG 30.55 ±2.63a 8.13 ±0.66a 5.33 ±0.43a 0.61 ±0.04a
AS 19.63 ±3.13b 4.90 ±0.94b 3.33 ±0.66a 0.51 ±0.05a
MP 25.08 ±2.55ab 7.31 ±0.77ab 5.00 ±0.54a 0.60 ±0.04a
Values in the columns corresponded to mean and standard error. Values followed by the same letter do not differ statistically (Fisher’s LSD
test, p< 0.05).
3.6. Arbuscular Mycorrhizal Fungi and Soil Properties
Three diversity indexes (inverse Simpson (1/D), exponential Shannon (ExpH
), and even-
ness) were negatively correlated with pH, Ca and Mg (r<
0.64; p< 0.05),
two diversity
(1/D and ExpH
) were negatively correlated with P (r<
0.65; p< 0.05), and the VT richness
was negatively correlated with Ca (r=0.72; p< 0.05) (Table S4, Supplementary Materials).
Redundancy analysis (RDA) of AM fungal communities associated with soil variables
(inertia proportion constrained = 23.77%) showed a clear separation of MP from the
other rubber plantations (Figure 8a). The AM fungal communities on MP were strongly
associated with a higher soil Na content (Figure 8b), where Glomus VT269 was favored by
this condition. RDA plot also showed that the AM fungal communities on CTCG were
associated with sandier soils (Figure 8a), where Glomus VT280 was favored by soils with
coarse texture. There was a weak relationship between the AM fungal community on
CTCG and P (Figure S1, Supplementary Materials).
Agriculture 2021,11, 361 12 of 17
Figure 8.
) Redundancy analysis (RDA) of AM fungal communities associating with rubber tree
plantations, constrained by soil variables. Blue arrows indicate significant soil variables for the
constrained ordination (p< 0.05). Red arrows indicate significant AMF VT species with maximum
correlation with ordination scores (r
0.5; p< 0.05). Ellipses indicate one standard deviation around
the centroid position of each rubber tree plantation. (
) Redundancy analysis (RDA) of AM fungal
communities associated with rubber tree plantations according to Na soil gradient.
4. Discussion
Rubber planted on degraded soils of the Colombian Amazon harbored highly diverse
AM fungal communities. The AM fungal communities in rubber roots differed among the
plantation types but not between the rubber genotypes.
The molecular approach to assess AM fungal community composition was more
sensitive than the soil-borne spore approach. The molecular approach recorded a higher
number of AM fungi from the Archaeosporaceae and Gigasporaceae families. The Ar-
chaeosporaceae and Gigasporaceae families produced low numbers of large-spore size [
than the Glomeraceae family, which was the best represented and most diverse in the study
area (with 77% of the total AM fungal community). Additionally, the molecular approaches
provided information for the presence of AM fungi that do not sporulate frequently or do
not sporulate at all [
], offering a more accurate picture of the AM fungal community. The
AM fungal community in rubber roots was composed of 135 VT in 13 genera. There was a
higher number of AM fungi associated with rubber roots than in previous studies (
111 VT
of 10 genera [
]), even on the rubber plantations planted on areas previously covered by
pastures (on average, 22 VT of 7 genera per plot; 16 VT of 5 genera per plot [
]). It is
important to indicate that this is the first study evaluating the AM fungal composition of
rubber roots using WANDA and AML2 primers, which limits comparisons with results
from previous publications. Differences in the number of VT between this study and others
Agriculture 2021,11, 361 13 of 17
might have resulted from the molecular technique used to assess the AM fungi and should
not be interpreted as real differences.
Glomus was the dominant genus, representing 66% of the total AM fungal community,
followed by Acaulospora, Paraglomus, and Archaeospora.Glomus and Acaulospora were
reported previously as frequent genera associated with rubber [
], and the main genera
composing the AM fungal community of Amazon soils [4648].
In the study area, rubber plantations were planted on degraded pastures after years of
cattle ranching. Soils where rubber tree grows presented low fertility, with very low levels
of available P and significant differences in the amount of Na among plantations. Pfeiffer
and Bloss [
] found that phosphate fertilizers included low concentrations of Cu, Zn, Na,
K, and SO
and were a source of those elements. A significantly higher amount of Na on the
older plantations (AS and MP) might have resulted from periodical fertilization in earlier
years and later soil accumulation. MP and AS also had significantly higher percentages of
root colonization (66% and 57%, respectively). Higher percentages of root colonization in
MP and AS might have been the consequence of an accumulative effect from fertilization,
through which Na, in combination with P, increased the AM root colonization [
]. On the
other plantations, rubber roots presented percentages of AM root colonization around 47%,
similar to previous reports [50].
The AM fungal richness and diversity (ExpH
) were significantly higher in CTIG and
MP than in the other plantation types. Feldmann et al. [
] found lower spore diversity
on commercial rubber plantations than in natural tree stands. They attributed differences
to agronomic practices on commercial plantations and mainly to the use of pesticides
and extensive weeding. Although there were differences in the agronomic practices used
on the different rubber plantations (e.g., MP received less fertilization than the other
plantations), our results are best explained by differences in age between rubber plantations.
Plantations over nine years old (MP and CTIG) had higher AM fungal richness and diversity
than younger plantations. Even with the limitations to compare results obtained from
different molecular techniques, our result was similar to the one reported by Herrmann and
collaborators. Herrmann et al. [
] also found differences in AM fungal richness related to
plant age in a rubber chronosequence of 3, 6, and 16 years old. The NMDS analysis clearly
showed how the AM fungal community composition of very old rubber plantations was
sufficiently different from the others, forming a separate cluster (Figure 6). Additionally,
the low numbers of AM fungal spores in MP resembled the abundance of AM fungal
spores in soils of mature Amazon forests [46].
Diversity indexes were negatively correlated with pH, Ca, Mg, and P. Similar results
had been reported previously for rubber plantations [
]. The edaphic condition is one of the
main factors affecting AM fungal community composition [
]. Soil pH has been clearly
identified as one of the most important abiotic drivers of AM fungal communities [
pH directly influences the availability of Ca, Mg, and P in soil. In soils with a low pH, P
became particularly less available as it is sorbed in insoluble compounds [
]. Some specific
AM fungi are commonly associated with acid soils, such as Acaulosporaceae, and some
Glomeraceae, such as Rhizophagus manihotis [
]. Particularly, Rhizophagus manihotis is
commonly associated with acidic poor-nutrient soils [56,57].
In clonal trials, selected Colombian rubber genotypes performed better (growth, early
latex production, and resistance to pathogens) than the IAN 873 (control) genotype [
Our results indicated that AM root colonization, richness, and composition of AM fun-
gal communities in roots of different rubber genotypes were similar, even if different
rubber genotypes (Colombian vs. IAN 873) were under the same conditions (location,
plantation type, and age). The AM fungal community composition in roots of Colom-
bian and introduced genotypes shared around 70% of the total community (Figure 7b).
Herrmann et al. [9]
identified four VT as indicator species for rubber, namely, Glomus
VT399, Acaulospora VT227, Rhizophagus manihotis VT90, and Glomus VT124. From those VT,
three were recorded in this study. Rhizophagus manihotis was one of the 20 more abundant
VT colonizing rubber tree roots. Glomus VT399 was an indicator species of introduced
Agriculture 2021,11, 361 14 of 17
rubber tree genotypes, and Acaulospora VT227 was an indicator species of MP, but both had
a low number of reads. The most abundant VT colonizing rubber roots was Paraglomus
VT444, which was not reported before in rubber tree roots. Paraglomus VT444 was an
indicator taxon of Colombian rubber genotypes and AS. This VT was isolated before in the
study area from pastures, and its abundance increased in soils of secondary forests that
originated from the natural regrowth of those pastures [
]. Since AS was similar to natural
secondary forests, Paraglomus VT444 persisted in AS soils. The particular association of
this VT with Colombian rubber genotypes might be related to the fact that the Colombian
genotypes were the youngest rubber trees and were cultivated on recently used pastures.
Rubber preferences for a particular AM fungal taxon were weak. Strong relationships
between particular AM fungi and rubber seem to be context dependent, varying from
one site to another. Apparently, plant host-AM fungal preferences occur at the plant
level (functional) groups [
] rather than at the level of individual plant species. Even
if grifting plants such as rubber tree clones behave as particular individuals [
], the
arbuscular mycorrhizal association would not be affected by genotypic differences between
genotypes. Rubber tree genotypes apparently behave as natural varieties, even if genotypic
variability was induced artificially. The similarity in arbuscular mycorrhization among
manioc varieties (Manihot esculenta Crantz), another important commercial Euphorbiaceae
species, has been reported [60], supporting the interpretation of our results.
According to Chen et al. [
], agroforestry systems for rubber trees are the best al-
ternative for improving soil properties. Our results indicated that none of the rubber
plantations improved the degraded condition of the soils. Significant differences in the soil
composition occurred only on rubber plantations older than 30 years. Herrmann et al. [
also found that the soil fertility of rubber plantations did not change over time despite
fertilization. Frequent weed control and other agronomic practices could be responsible for
this result. Although soil condition is not improved during the productive cycle of rubber,
its roots host significantly more AM fungi (in average 22 VT per plot) than other commercial
crops cultivated in Amazon, i.e., mahogany (Swietenia macrophylla; 19 VT [
]), eucalyptus
16 VT [10]
), and soybean (17 VT [
]). A higher AM fungal diversity will enhance the
external mycelial network, improving the nutrition of the plant community [
]. Addi-
tional traits (e.g., soil aggregation, soil organic C, biomass C sequestrated) and ecological
services (plant, enthomofauna, and bird diversity) have been evaluated on different rubber
plantations and genotypes [
], corroborating the importance of this plant species for
soil restoration.
Supplementary Materials:
The following are available online at
10.3390/agriculture11040361/s1, Table S1: Soil and rubber tree samples collected and analyzed,
Table S2
: Arbuscular mycorrhizal fungal virtual taxa recovered from different rubber plantations,
Table S3: Arbuscular mycorrhizal fungal virtual taxa with significant indicator species value for
rubber genotypes and plantation types, Table S4: Spearman’s correlation coefficients between soil pa-
rameters, and richness and diversity indexes of arbuscular mycorrhizal fungi, Figure S1: Redundancy
analysis (RDA) of arbuscular mycorrhizal fungal communities associated with rubber plantations
according to phosphorus soil gradient.
Author Contributions:
Conceptualization, C.P.P.-V. and A.S.; methodology, A.S., C.P.P.-V. and
.; software, A.S.; validation, C.P.P.-V. and A.S.; formal analysis, A.S. and C.P.P.-V.; investiga-
tion, C.P.P.-V.; resources, A.S. and C.P.P.-V.; data curation, T.K.A.-R. and A.S.; writing—original draft
preparation, C.P.P.-V.; writing—review and editing, C.P.P.-V. and A.S.; visualization, T.K.A.-R. and
A.S.; supervision, C.P.P.-V.; project administration, A.S.; funding acquisition, A.S. All authors have
read and agreed to the published version of the manuscript.
This study was funded by FCTeI-SGR, Contract 59/2013 Instituto Amazónico de Investiga-
ciones Científicas SINCHI–Gobernación del Caquetá–Universidad de la Amazonía–Asociación de
Reforestadores y Cultivadores de Caucho del Caquetá; and by the Government of Colombia through
the project BPIN 2017011000137 “Investigación en conservación y aprovechamiento sostenible de la
diversidad biológica, socioeconómica y cultural de la Amazonia colombiana.”
Agriculture 2021,11, 361 15 of 17
We thank Daniela León and Martti Vasar for their help with bioinformatic ana-
lyzes. We also thank all the farmers of the study area for their help and support during
the fieldwork.
Conflicts of Interest: The authors declare no conflict of interest.
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... Most studies are based on CATALOGUE OF FUNGI OF COLOMBIA spore number counts (e.g., Restrepo et al., 2019;Sandoval & Ordoñez, 2019), evaluation of mycorrhizal colonisation on roots (e.g., Restrepo et al., 2019), and identification of morphotypes based on spore morphology (e.g., Posada et al., 2018). However, during the past five years, there has been an increase in ecological studies using metagenomic approaches (Peña-Venegas et al., 2021). Questions regarding the influence of biotic and abiotic factors on AMF spore number, species richness, and species composition have been addressed in anthropogenic and natural ecosystems throughout the Colombian territory (e.g., López, 2009;Tirado-Ardila, 2017). ...
... Regarding AMF species richness and composition, Peña-Venegas et al. (2021), using molecular approaches in lowland rubber plantations, found that AMF species richness was negatively correlated with pH, Ca, Mg, and P. These authors also found that AMF species composition changed along a Na -availability gradient, with soil texture being also an important factor structuring the communities. ...
... Studies using metagenomic approaches have increased in recent years. A study done by Peña-Venegas et al. (2021) comparing traditional morphological and molecular approaches in rubber plantations in Caquetá found, with both approaches, that Glomeraceae was the dominant taxon. However, molecular data showed a higher diversity and more significant differences in species composition among sites when compared with spore morphotype analysis. ...
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Owing to its tropical location and great diversity of ecosystems, Colombia hosts a high diversity of fungi, which play fundamental roles in ecosystems as mycorrhizas, saprophytes, endophytes, and pathogens. In this chapter, we describe a literature review of ecological studies focusing on the most-studied fungal functional groups of Colombia: arbuscular mycorrhizas, ectomycorrhizas, saprotrophs, and endophytes. To complement the literature review, we used the University of Antioquia Herbarium (HUA) database, which includes more than 11,000 macrofungi specimens, to run alpha diversity and network analyses. The alpha diversity analyses were performed using species accumulation curves for the total number of specimens and specimens divided by ecosystem types (oak forests, mixed montane forests, Amazonian lowland forests, and extra-Amazonian lowland forests) and with diversity indexes based on Chao 1 and bootstrap estimators. Network analysis was based on correlation matrices among main ecosystem types. These analyses made it possible to compare the species richness and diversity patterns among the main ecosystem types. Our results show a high number of collections of ectomycorrhizal fungi from oak forests, which are typical of this type of ecosystem, and a high alpha diversity for Colombia's Amazonian lowland forests. We highlight significant knowledge gaps regarding ecological research in the country as the diversity patterns of many functional groups of fungi are still unknown. We recommend increasing the number of studies based on environmental sequencing techniques because these will allow the inclusion species of microfungi. RESUMEN Colombia por su ubicación en la región tropical y su gran diversidad de ecosistemas, favorece una alta diversidad en hongos, los cuales son fundamentales en los ecosistemas dado que juegan papeles importantes como hongos micorrízicos, saprófitos, endófitos y patógenos. Para el presente trabajo se realizó una revisión de literatura de estudios ecológicos enfocados en los grupos funcionales de hongos más estudiados en el país. Para complementar la información obtenida en la revisión de literatura, se utilizó la base de datos del herbario de la Universidad de Antioquia (HUA), la cual incluye más de 11.000 colecciones de macrohongos, para realizar análisis de diversidad alfa y análisis de redes. Los análisis de diversidad alfa se realizaron con curvas de acumulación de especies para el total de las colecciones y para las colecciones divididas por tipos de ecosistemas (bosque de roble, bosque montano mixto, tierras bajas amazónicas y otras tierras bajas) y con estimadores de diversidad basados en Chao 1 y análisis de bootstrap. Los análisis de redes se realizaron con base en matrices de correlación entre los principales ecosistemas. Con estos análisis fue posible comparar la riqueza de especies entre los principales tipos de ecosistemas, y a su vez se pudo identificar los principales patrones de diversidad beta para el país. Los resultados muestran una alta diversidad alfa para los bosques amazónicos de tierras bajas del país, ya que con menor número de colecciones se obtuvo un número total de 524 especies, con un número estimado de especies entre 638 y 975. Además, se observó un elevado número de especies (474) en los bosques de roble en su mayoría representados por especies ectomicorrízicas, lo que lo posiciona en el segundo ecosistema más rico en especies de hongos del país con una riqueza estimada de especies entre 566 y 847. Los análisis de redes mostraron un bajo número de especies compartidas entre los bosques de roble y los demás ecosistemas; mientras que los bosques montanos mixtos y los bosques de tierras bajas comparten un número alto de especies. Nuestros resultados muestran la existencia de grandes vacíos de información en cuanto a investigación ecológica en el país, ya que aún se desconocen los patrones de diversidad de muchos grupos funcionales de hongos. En especial, se recomienda realizar estudios basados en técnicas de secuenciación de muestras ambientales, ya que estos permitirán incluir especies de microhongos los cuales no pueden ser estudiados con el uso de colecciones de herbario.
... Glomus is generally more resistant to many kinds of disturbance in comparison with other genera (van der Heyde et al. 2017) and is very competitive colonizing roots due to the high number of propagules that produce (Klironomos and Hart 2002), and therefore, Glomus is more common in disturbed ecosystems such as those introduced pastures. The genus Paraglomus is commonly abundant in tropical forest ecosystems (García de León et al. 2017;Marinho et al. 2018;Peña-Venegas et al. 2021), which explains why it became an important genus in the AM fungal composition of the Amazon forest. ...
... Mycorrhized root samples were obtained at the moment of manioc harvesting. For the rubber tree, we included data from 19 different rubber clones (nine native clones and ten introduced clones) cultivated in clonal banks in four different soil types (Peña-Venegas et al. 2021). Mycorrhized root samples were obtained from 9-year-old rubber trees. ...
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Mycorrhizal associations are poorly studied in tropical environments, including the Amazon region. This chapter discusses advances and limitations with a historical perspective on arbuscular mycorrhizal (AM) associations in the Colombian Amazon, based on the analysis of more than 1200 samples collected during the last decade. This data provides insights into the arbuscular mycorrhizal fungal diversity and richness trends across the Colombian Amazon, including their relationship with the ongoing deforestation activities. This chapter also addresses particular information about the arbuscular mycorrhization of two important plant species from the Euphorbiaceae: the manioc (Manihot esculenta) and the rubber tree (Hevea brasiliensis). These species were analyzed more in depth given their relevance to the local economy, raising new questions about the arbuscular mycorrhization of phylogenetically related plant species. Overall, the data and molecular analyses performed in the last decade clearly indicate a fast evolution in the recommended and available molecular approaches. In turn, this has generated serious limitations on the comparison among samples due to the different use of primers and sequencing methods. Undoubtedly, this chapter presents the most complete overview of the arbuscular mycorrhizal fungi described in the Colombian Amazon region, an extension of 483.164 km2 of the upper Amazon basin.KeywordsFungal diversityGlomeromycotaNext-generation sequencingState of the artUpper Amazon region
... Each library was ligated to Illumina adaptors, using the TruSeq DNA PCR-free library prep kit (Illumina Inc., San Diego, CA, USA) and sequenced on the Illumina MiSeq platform, using a 2 × 300 bp paired-read sequencing approach. Sequencing was done at the Asper Biogene laboratory (Tartu, Estonia) as described by Peña-Venegas et al. [28]. ...
... A reduction of Glomus abundance in the soil during the successional regrowth might reflect less stressing environmental conditions that reduced the need of Glomus to sporulate [16]. Paraglomus has been associated with forested areas [14,20,28] and its increasing abundance in the soil during the successional regrowth could reflect the preference of this genus for more diverse and forested environments. These two particular changes in the AM fungal community composition over the successional chronosequence might be considered signals of environmental restoration. ...
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Natural restoration of ecosystems includes the restoration of plant-microbial associations; however, few studies had documented those changes in tropical ecosystems. With the aim to contribute to understand soil microbial changes in a natural regrowth succession of degraded pastures that were left for natural restoration, we studied changes in arbuscular mycorrhizal (AM) fungal communities. Arbuscular mycorrhizal fungi (AMF) establish a mutualistic symbiosis with plants, improving plant nutrition. Amplification of the small subunit rRNA with specific primers and subsequent Illumina sequencing were used to search soil-borne AM fungal communities in four successional natural regrowth stages in two landscapes (hill and mountain) with soil differences, located in the Andean-Amazonian transition. Molecular results corroborated the results obtained previously by spores-dependent approaches. More abundance and virtual taxa of AMF exist in the soil of degraded pastures and early natural regrowth stages than in old-growth or mature forest soils. Although changes in AM fungal communities occurred similarly over the natural regrowth chronosequence, differences in soil texture between landscapes was an important soil feature differentiating AM fungal community composition and richness. Changes in soil-borne AM fungal communities reflect some signals of environmental restoration that had not been described before, such as the reduction of Glomus dominance and the increase of Paraglomus representativeness in the AM fungal community during the natural regrowth chronosequence.
... This taxon is recognized for its broad versatility, which gives it the ability to colonize various plant roots without needing a specific affinity. Additionally, the higher presence of Paraglomus in the soils of Palmira for both plants could be linked to factors of the plant growth environment since the genus has been associated with soils rich in plant diversity and forested areas [49,50]. Moreover, the higher abundance of Diversispora in Sibundoy for L. alba, compared to other sampling points, could be associated with reduced precipitation levels, which have previously been described as a factor for the genus's high abundance and potentially diminishing the dominance of Glomus [51]. ...
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Medicinal plants maintain structures and diversities of bacteria, fungi, and arbuscular mycorrhizal fungi (AMF) that can interact to promote growth and therapeutic properties. Therefore, the purpose of this research was to evaluate the microbiome of Lippia alba and Petiveria alliacea, species known for their high potential for medicinal benefits in Colombia. To achieve this, rhizosphere soils and roots were sampled from five departments in Colombia: Boyacá, Cundinamarca, Tolima, Putumayo, and Valle del Cauca. The results revealed that the dominant bacterial groups in both plants were primarily Proteobacteria, Acidobacteriota, and Actinobacteriota, with the first phylum showing the highest number of differentially abundant genera between the sampling points. In fungi, Ascomycota tended to dominate in most of the sampled locations, while Mortierellomycota was particularly abundant in roots of P. alliacea in Valle. Furthermore, the study of AMF indicated differentiation in the colonization for both plants, with the genera Glomus and Paraglomus being predominant. Differences in the Shannon diversity index were recorded between sampling types within these sampling points, possibly influenced by local and environmental factors. Our findings reveal that the microbiomes of both medicinal plants exhibit distinct community assemblies, which could be a significant factor for their future therapeutic use.
... The highest reduction in weed suppression indicated by the lowest amount of weed biomass had been observed from the 3 L ha -1 +15 g ha -1 combined herbicide glyphosate+metsulfuron-methyl treatment group. The eradicated weed changes the moisture and temperature of the soil surface which in turn affects the activity of soil microbes (Peña-Venegas et al. 2021;Tall and Puigbò 2022), enzymes (Chaudhary et al. 2021;Tyler 2022), and macrofauna (Lacava et al. 2021). Weeds have been known as an alternate host for some pests and pathogens; hence changes in weed population results in changes in some soil macrofauna. ...
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Chaniago I, Yulistriani, Umami IM, Bukhari ZZ. 2023. Soil macrofauna diversity and weed dynamics in response to different methods of weed control in smallholder rubber farming. Biodiversitas 24: 3106-3113. Weeds interference in rubber farmland may reduce latex yield. Farmers apply herbicides to control weeds. However, the herbicide not only controls weed but also affects the presence of soil macrofauna. A study has been conducted to determine the effect of different method of weed control on soil macrofauna and weeds at smallholder rubber farming at Pulau Punjung, Dharmasraya District, West Sumatra, Indonesia. The experiment was conducted in a completely randomized block design with 6 treatments and 4 pseudo-replications. Treatment was mechanical control, without weed control, and 4 doses of herbicide glyphosate+metsulfuron-methyl (1.5 L ha-1 + 15 g ha-1, 2 L ha-1 + 15 g ha-1, 2.5 L ha-1 + 15 g ha-1, 3 L ha-1 + 15 g ha-1) with 400 L ha-1 of volume. Pitfall traps were used to collect the soil macrofauna. Data were analysis with ANOVA for weed and soil macrofauna in response to different methods of weed control. Results demonstrated that the application of glyphosate+metsulfuron-methyl herbicide significantly suppressed weeds higher than that of other methods of weed control (p<0.05). Para grass (Brachiaria mutica (Forssk.) Stapf) was the most dominant weed but has been affected most by 3 L ha-1 + 15 g ha-1 herbicide mixture. Soil macrofauna of the order Hemiptera was affected most by the application of herbicide with a total reduction of 71.58% of number of individuals at 12 weeks after application of herbicide. In general, different weed control methods resulted in varied numbers of orders and individuals of the soil macrofauna.
... Arbuscular mycorrhizae (AM) use as biological agents to reduce chemical fertilizers use (El-Sherbeny et al, 2022;Trejo et al., 2021), increase of water use efficient (Begum et al., 2019;El-Tohamy et al., 2021), and increase nutrient absorption (Begum et al., 2019; has been researched and applied to various horticultural crops (Golubkina et al., 2020;Karti et al., 2021), food crops (Campo et al., 2020;Addo et al., 2020), plantation crops (Fajariza et al., 2020;Pena-Venegas et al, 2021;Rini et al., 2021), fodder forage crops (Rosita et al., 2020;Karti et al., 2021) and afforestation crops (Aji et al., 2021;Husna et al., 2021). However, the use of biocompost fertilizer has not been widely applied by Allium cepa farmers by utilizing microorganisms as biological agents to absorption maximized of nutrients contained in the bio compost. ...
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Synthetic technology application in the planting center of onion (Allium cepa L) Enrekang district, Indonesia, has passed the threshold recommendation dosage of manufacturer and agricultural extension. The synthetic fertilizer application with high dosage and inefficient nutrient absorption by plants is a problem that must be solved. So that, the proposed solution hypothesis is the application of biocompost enriched with Arbuscular Mycorrhizae (AM) as biological agents can reduce synthetic fertilizers use and absorption nutrients increase by plants. The aim of research to determine the growth of Allium cepa given dosage of biocompost enriched with AM, and research novelty are modification of innovation biocompost with AM as biological agent for growth of Allium cepa. The research was conducted for six months using model of Randomized Block Design. The treatment dosage of biocompost enriched with AM, are BM0 (control: Allium cepa planting method of local farmers); BM1 (Dosage of biocompost 100 kg.plot-1+ AM); and BM2 (Dosage of biocompost 200 kg.plot-1+AM), enrichment of biocompost with AM was carried out by mixing 2 kg of AM propagules for each treatment. The observed research variables are leaves number, root length, root diameter, root surface area, and tuber number. Observational data in the field and laboratory were analyzed using analysis of variance and Duncan's test. The results showed that the biocompost at a dose of 200 kg.plot-1 enriched with AM showed better growth in leaf number, root length, root diameter, root surface area, and the number of tubers compared to other treatments. So that the application of biocompost at a dose of 200 kg.plot-1 is the main finding in this study and can be recommended as a good dose for the production of Allium cepa which is environmentally friendly. This research supports sustainable and environmentally friendly agricultural systems which are the scope of healthy future agriculture.
... The soil ecosystem in the BLA is strongly linked with some plant-traits, such root growth, litter deposition, and plant biomass production that make up the monospecific stands from the Brazil's Legal Amazon (Chaves et al. 2020). The soil ecosystem is also recognized with a natural low fertility in the major portion of the BLA (Sátiro et al. 2021;Peña-Venegas et al. 2021). Into this context, the nutrient cycling, and symbiotic association through a diverse soil food web are the main factors that promote plant performance at monospecific stands (Celentano et al. 2020;Vasco-Palacios et al. 2020). ...
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Many endemic plant species from Brazil's Legal Amazon present soil organisms in their rhizosphere. These organisms play a key role in the physiological traits, plant performance, and resistance against drought, and herbivory. Our aim here was to present a quantitative analysis of the arbuscular mycorrhizal fungi (AMF) species, and soil nematodes associated with endemic plant species from the Brazil's Legal Amazon, Rio Branco, Acre. We found four main groups considering the similarities on soil microbiota community structure: i) T. cacao, M. flexuosa, and G. weberbaueri showed high AMF and soil nematode richness; ii) S. officinarum and V. unguiculata showed high herbivore nematode abundance and low Ambisporaceae and Clar-oideoglomeraceae sporulation; iii) H. brasiliensis and E. guineensis showed the low abundance of Gigasporaceae spores and lack of herbivore nematodes; and iv) E. precatoria showed the high abundance of A. colombiana, Monanchus, and Tripyla. The results of our study highlight the importance of considering endemic tree species as potential hosts for a solid and diverse soil food web on a sustainable way to improve soil ecology, root traits, and plant performance. Thus, long-term experiments considering these endemic tree species into agroforestry systems may exploit interesting results in tropical conditions.
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Abstract Reclamation of oil and gas disturbed soils is challenging due to diminished function (i.e., soil physical, chemical, and biological properties) from the loss of soil organic carbon (SOC) and potential mixing of topsoil and subsoil. Biostimulants are agro‐products applied to soil to improve SOC formation, microbial nutrient cycling, and crop yields, suggesting their potential use in reclaiming oil and gas disturbed soils. However, studies on the ability of biostimulants to enhance reclamation in disturbed soils are limited. Therefore, research was conducted to determine if biological properties were affected by biostimulant products in soil collected from an active pipeline installation project. The study was conducted in a greenhouse using pots consisting of the following soil treatments: TS100 (100% topsoil), TS50 (1:1 by‐weight subsoil/topsoil), TS25 (3:1 subsoil/topsoil), TS12.5 (7:1 subsoil/topsoil), and TS0 (100% subsoil). Blended soil either received a liquid inoculant or biotic mulch biostimulant and were planted with hard red spring wheat (Triticum aestivum) later on. Soil biological properties were generally influenced by topsoil concentration where TS50 consistently produced similar results to TS100, however, nitrogen (N) and phosphorus (P) were also influenced by biostimulant treatment. Additionally, wheat biomass was significantly greater in the liquid treatment, whereas the biotic mulch stimulated greater microbial abundance and activity. Overall, increased topsoil improved biological recovery in the short term, and the addition of biostimulants in blended soils can also enhance recovery regardless of topsoil content. However, it is unclear whether the recovery is sustained into the long‐term without additional biostimulant application.
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The arbuscular mycorrhizal (AM) fungi are a globally distributed group of soil organisms that play critical roles in ecosystem function. However, the ecological niches of individual AM fungal taxa are poorly understood. We collected > 300 soil samples from natural ecosystems worldwide and modelled the realised niches of AM fungal virtual taxa (VT; approximately species‐level phylogroups). We found that environmental and spatial variables jointly explained VT distribution worldwide, with temperature and pH being the most important abiotic drivers, and spatial effects generally occurring at local to regional scales. While dispersal limitation could explain some variation in VT distribution, VT relative abundance was almost exclusively driven by environmental variables. Several environmental and spatial effects on VT distribution and relative abundance were correlated with phylogeny, indicating that closely related VT exhibit similar niche optima and widths. Major clades within the Glomeraceae exhibited distinct niche optima, Acaulosporaceae generally had niche optima in low pH and low temperature conditions, and Gigasporaceae generally had niche optima in high precipitation conditions. Identification of the realised niche space occupied by individual and phylogenetic groups of soil microbial taxa provides a basis for building detailed hypotheses about how soil communities respond to gradients and manipulation in ecosystems worldwide.
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El caucho [Hevea brasiliensis (Willd. Ex Adr. de Juss.) Muell.-Arg.] es una especie de origen suramericano productora de látex destinado principalmente a la industria llantera (Compagnon, 1998). Dada la importancia del caucho natural y su creciente demanda en el mercado internacional, en Colombia se han venido adelantando planes masivos para la expansión del cultivo la mayoría de ellos apoyados en el establecimiento de nuevas hectáreas en pequeños y medianos cultivadores cuya estrategia busca en general, compensar en primer lugar la demanda interna. Según CCC (2017) en el último censo cauchero realizado en 2015 se reportaron 53.223 ha en Colombia de las cuales cerca de 5.000 ha se encuentran en el departamento del Caquetá, Amazonia colombiana. En Colombia, todas las plantaciones comerciales se han establecido con clones introducidos y en regiones como el Caquetá el fomento y desarrollo del cultivo de caucho se ha limitado históricamente al uso de tres clones (Castellanos et al., 2009). Esta reducida base genética y las condiciones ambientales y culturales limitantes han afectado la productividad y la competitividad del sector cauchero en el Caquetá (Asoheca, 2010). En este sentido, el Instituto Amazónico de Investigaciones Científicas SINCHI, la Universidad de la Amazonía y la Asociación de Reforestadores y Cultivadores de Caucho del Caquetá Asoheca han contribuido en Caquetá con información preliminar sobre la ampliación de la base genética de caucho con nuevos materiales promisorios a través de la evaluación preliminar de genotipos regionales élite (Sterling y Rodríguez, 2011, 2017, 2018) y de clones promisorios introducidos a la región (Sterling y Rodríguez, 2012, 2017, 2018), como una de las principales estrategias con que necesita la región para fortalecer y sustentar mediante la investigación científica la competitividad del sector cauchero en el Caquetá para los próximos 50 o 60 años. No obstante, la sostenibilidad productiva del cultivo del caucho no sólo depende del tipo de material genético, sino que además está influenciada por diversos factores ambientales entre los que destaca la capacidad de los sistemas de producción con cacuho para proveer bienes y servicios ambientales de interés agroambiental. Por ello, otros aspectos de interés a evaluar en los nuevos clones es su capacidad de promover condiciones que permitan conservar la biodiversidad, recuperar los suelos degradados, mitigar los efectos del cambio climático, entre otros. En este documento se presentan las bases técnicas para la valoración y el análisis de los principales recursos de la biodiversidad (avifauna, entomofauna e indicadores biológicos de suelos) y el servicio ecosistémico de secuestro de carbono, asociados a campos clonales de caucho con materiales genéticos promisorios para el departamento del Caquetá y con potencial para la región amazónica colombiana. Esta publicación está dirigida principalmente a productores y técnicos de caucho, estudiantes y profesionales del sector, como una herramienta didáctica que busca valorar y analizar la importancia de estos nuevos materiales genéticos de caucho por su capacidad para proveer bienes y servicios ecosistémicos en el Caquetá, mediante la evaluación agroambiental a pequeña y a gran escala de nuevos clones con potencial para la Amazonía colombiana.
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Manioc (Manihot esculenta Crantz) is an important tropical crop that depends on arbuscular mycorrhizal (AM) association for its nutrition. However, little is known about the richness and species composition of AM fungal communities associating with manioc and possible differences across soils and manioc landraces. We studied the diversity and composition of AM fungal communities present in the roots of different manioc landraces and surrounding soils in indigenous shifting cultivation fields on different Amazonian soil types. A total of 126 AM fungal virtual taxa (VT; phylogenetically defined taxonomic units) were recovered from soil and root samples using 454 sequencing of AM fungal SSU rRNA gene amplicons. Different AM fungal communities occurred in different soil types. Minor differences occurred in the composition of AM fungal community associating with different manioc landraces, but AM fungal richness was not different among them. There was a low similarity between the AM fungal communities colonizing manioc roots and those recorded in the soil, independently of differences in soil properties or the manioc landrace evaluated. Rhizophagus manihotis and Glomus VT126 were the most abundant AM fungal species colonizing manioc roots. Contrasting with the results of earlier spore-based investigations, all the AM fungi identified as indicator species of particular manioc landraces were morphologically unknown Glomus species. In conclusion, different manioc landraces growing in common conditions associated with distinct AM fungal communities, whereby AM fungal communities in soils did not necessarily reflect the AM fungal communities colonizing manioc roots.
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Offspring size is a key trait for understanding the reproductive ecology of species, yet studies addressing the ecological meaning of offspring size have so far been limited to macro-organisms. We consider this a missed opportunity in microbial ecology and provide what we believe is the first formal study of offspring-size variation in microbes using reproductive models developed for macro-organisms. We mapped the entire distribution of fungal spore size in the arbuscular mycorrhizal (AM) fungi (subphylum Glomeromycotina) and tested allometric expectations of this trait to offspring (spore) output and body size. Our results reveal a potential paradox in the reproductive ecology of AM fungi: while large spore-size variation is maintained through evolutionary time (independent of body size), increases in spore size trade off with spore output. That is, parental mycelia of large-spored species produce fewer spores and thus may have a fitness disadvantage compared to small-spored species. The persistence of the large-spore strategy, despite this apparent fitness disadvantage, suggests the existence of advantages to large-spored species that could manifest later in fungal life history. Thus, we consider that solving this paradox opens the door to fruitful future research establishing the relationship between offspring size and other AM life history traits.
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The arrival of 454 sequencing represented a major breakthrough by allowing deeper sequencing of environmental samples than was possible with existing Sanger approaches. Illumina MiSeq provides a further increase in sequencing depth but shorter read length compared with 454 sequencing. We explored whether Illumina sequencing improves estimates of arbuscular mycorrhizal (AM) fungal richness in plant root samples, compared with 454 sequencing. We identified AM fungi in root samples by sequencing amplicons of the SSU rRNA gene with 454 and Illumina MiSeq paired-end sequencing. In addition, we sequenced metagenomic DNA without prior PCR amplification. Amplicon-based Illumina sequencing yielded two orders of magnitude higher sequencing depth per sample than 454 sequencing. Initial analysis with minimal quality control recorded five times higher AM fungal richness per sample with Illumina sequencing. Additional quality control of Illumina samples, including restriction of the marker region to the most variable amplicon fragment, revealed AM fungal richness values close to those produced by 454 sequencing. Furthermore, AM fungal richness estimates were not correlated with sequencing depth between 300 and 30,000 reads per sample, suggesting that the lower end of this range is sufficient for adequate description of AM fungal communities. By contrast, metagenomic Illumina sequencing yielded very few AM fungal reads and taxa and was dominated by plant DNA, suggesting that AM fungal DNA is present at prohibitively low abundance in colonised root samples. In conclusion, Illumina MiSeq sequencing yielded higher sequencing depth, but similar richness of AM fungi in root samples, compared with 454 sequencing.
In Latin America, there are areas that favor the cultivation of rubber (Hevea brasiliensis) and reduce the risk of South American Leaf Blight (SALB), produced by the pathogen Pseudocercospora ulei. This study aimed to analyze the growth, early yielding and SALB resistance of nine promising clones and IAN 873 (control) in the pre-tapping and early tapping phases in a large-scale clone trial in a low SALB pressure zone in the Colombian Amazon, 2010-2019. San Vicente del Caguán (Caquetá) has climatic characteristics that are not very favorable for SALB (mean precipitation < 2,600 mm year-1 and average relative humidity < 82%). After 10 years, the better clones (FX 3899 P1, FDR 4575, FDR 5578, GU 198 and FDR 5597) presented an acceptable average for the main trunk circumference (CMT < 52 cm) at the end of the pre-tapping phase (9th year), a favorable CMT (< 58 cm) in the early tapping phase (1st year tapping or 10th year), a superior early dry rubber yield (EDRY) (< 43 g.tree-1.tap-1), a high partial resistance to SALB (low severity, with mean scores for AT1 and AT2 < 1 and low asexual and sexual sporulation, with mean scores for TR and ST < 1) and a high percentage of leaves retained in the canopy (80 - 100%), as compared to clone IAN 873. This study provides the basis for final clonal selection once peak yield (5th year tapping) is identified for later development in the Amazon region, Colombia.
As anthropic transformation of Amazonian rainforests into degraded lands continues, the consequences of this on arbuscular mycorrhizal fungi (AMF) remain in the dark. This paper describes changes in AMF (glomerospore abundances, species composition and diversity and glomalin contents) along secondary forest succession, and we explore the impacts of seasonality and of soil texture and chemistry. Research was conducted in a shifting cultivation region at the eastern periphery of Amazonia, in ‘young’ (3–4 yrs old – SEC1) and ‘mid-aged’ (6-8yrs old –SEC2) degraded secondary forest regrowth, and in mature (>120yrs old – SEC3) rainforest, both in dry (November 2015) and in rainy (May 2016) seasons. We identify a total of 36 AMF species, corresponding to 24.1% of Braziĺs and 12.5% of the worldwide known AMF species richness. The genera Glomus and Acaulospora predominated in both seasons and over all successional stages, in terms of species richness and of relative abundances and frequencies. Though AMF species diversity did differ significantly between young / mid-aged degraded secondary forests and >120 yrs-old mature rainforests, differences were altogether small and – contrary to vegetation species diversity – higher in stages SEC2 + 3 than in SEC1. Neither easily-extractable nor total glomalin contents differed significantly between seasons or successional stages, though they did contribute substantially (overall 2.5% average) to total soil organic carbon. BCA suggests that AMF species composition was driven mainly by seasonality (15.9%) and only marginally (though likewise significantly) by succession (8.0%). A subset of soil variables (pH, OM, Al, CEC, Ca) related strongly (r2 = 0.46) with glomerospore abundance and AMF species composition. Our results support the view of a remarkably resilient limited set of AMF species with only subtle differences between young (degraded) secondary regrowth and mature rainforests. Thus, the successional trajectories of vegetation recovery after repeated shifting cultivation cycles are likely not limited by AMF species availability.
Arbuscular mycorrhizal (AM) fungi are obligate plant symbionts that have important functions in most terrestrial ecosystems, but there remains an incomplete understanding of host‐fungus specificity and the relationships between species or functional groups of plants and AM fungi. Here, we aimed to provide a comprehensive description of plant‐AM fungal interactions in a biodiverse semi‐natural grassland. We sampled all plant species in a 1000 m2 homogeneous plot of dry calcareous grassland in two seasons (summer and autumn) and identified root‐colonizing AM fungi by SSU rDNA sequencing. In the network of 33 plant and 100 AM fungal species, we found a significant effect of both host plant species and host plant functional group on AM fungal richness and community composition. Comparison with network null models revealed a larger‐than‐random degree of partner selectivity among plants. Grasses harbored a larger number of AM fungal partners and were more generalist in partner selection, compared with forbs. More generalist partner association and lower specialization were apparent among obligately, compared with facultatively, mycorrhizal plant species and among locally more abundant plant species. This study provides the most complete dataset of co‐occurring plant and AM fungal taxa to date, showing that at this particular site, the interaction network is assembled non‐randomly, with moderate selectivity in associations between plant species and functional groups and their fungal symbionts. This article is protected by copyright. All rights reserved.
Arbuscular mycorrhizal fungi (AMF) are a key component of soil microbiota in natural and anthropogenic ecosystems. Even though soil type and climate conditioned land uses in the past, soybean cultivation has overrode such limitations and replaced the earlier diverse agro-and natural ecosystems in many countries of South America. We investigated whether actual diversity patterns of local AMF communities were determined by previous land uses and their intrinsic environmental conditions. We sequenced AMF DNA from root and soil samples collected from current soybean fields with three historical land use situations (HLU): agricultural fields, livestock farming and forest sites. We detected overall high AMF richness: 87 virtual taxa (VT) in soil and 69 VT in soybean roots. Mean number of VT per sample ranged from 8.1 to 19.2; it was not affected by HLU nor type of sample, but correlated with soil texture, pH, and plant density. Conversely, AMF community composition did significantly diverge among HLU and type of sample. A distinctive community composition was observed in roots of historical agricultural fields which differed from any other soil and root sample evaluated in this study. We attribute this finding to variations in the abundance pattern of predominant AMF taxa (Glomeraceae and Gigasporaceae). Our results indicate that soybean cultivation supports relatively high AMF diversity, with apparent legacies from earlier management and natural habitats in the composition of resident AMF communities.