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Global Soil Biodiversity Atlas

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Abstract

Key messages • Soil is an important habitat for thousand millions of organisms. • Soil biodiversity is extremely diverse in shapes, colours, sizes and functions. • Soil biodiversity is globally distributed, from deserts to polar regions through grasslands, forests, urban and agricultural areas. • Soil biodiversity supports many services essential to human beings: plant growth, water and climate regulation, and disease control, among others. • Soil biodiversity is increasingly under threat due to several pressures acting on soils. • Interventions to reduce the impact of threats to soil biodiversity are available and should be widely adopted. • Policies to protect and value soil biodiversity are still at an early stage and need to be further developed. http://esdac.jrc.ec.europa.eu/content/global-soil-biodiversity-atlas
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... Microbial communities in the soil play a crucial role in the multifunctionality of terrestrial ecosystems. Being one of the most diverse habitats on Earth, the soil harbors millions of individuals and thousands of bacterial species in a single gram (Orgiazzi et al., 2016). Due to their sensitivity to deficient or excessive levels of PTMs, microorganisms serve as bioindicators for assessing contaminated sites, swiftly detecting environmental changes caused by contamination (Kabata-Pendias, 2011;Parmar et al., 2016), and their ability to retain contaminants and survive adverse conditions enhances their suitability for that key factor. ...
... The percentages were lower, ranging from 27.5 to 38.5% in PE5%, PE + BC5%, CO + BC5%, PE + CO + BC5%, soil, and CO and lower than 6.5% in PE + CO5%, PE, and BC. It is the largest and most diverse phylum, containing approximately 30% of the total number of bacterial species (Orgiazzi et al., 2016). Its predominance is consistent with results from previous studies for metal-contaminated soils (Kasemodel et al., 2019b;Liu et al., 2021;Qi et al., 2022;Xiao et al., 2022;Zhao et al., 2019) and improved contaminated ones (Hong et al., 2022;Li et al., 2020;Xu et al., 2021) and bacteria are gram-negative and more tolerant to metal contamination compared to gram-positive ones (Wang et al., 2010). ...
... It was predominant not only in the slag (which had the highest concentrations of contaminants), but also in the enhanced samples and those containing all three reactive materials (controls that were not contaminated). Actinobacteriota include gram-positive bacteria with a wide diversity of morphologies, ranging from micrococci (spherical) to rods and to branched filaments that resemble fungal hyphae (Orgiazzi et al., 2016). The phylum was dominant in soils contaminated with small concentrations of metals (Liu et al., 2021) and one of the three dominant phyla in multi-contaminated soils (Qi et al., 2022). ...
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Soil amendments have emerged as a crucial remediation strategy. However, the effects of improvements on tropical soils contaminated by potentially toxic metals and metalloids (PTMs) in mining areas remain largely unknown. This paper reports on a pot experiment conducted with peat, compost, and biochar, together with soil and slag containing high concentrations of PTMs from an abandoned mine site (Ribeira Valley, Brazil). Mixtures of slag, soil, and amendments altered the geochemical fractionation and, in most improvements, resulted in positive changes in maize (Zea mays) growth, which may be due to the lower bioavailability of contaminants and/or the greater supply of nutrients. The germination rate was less sensitive to the effect of the improvements, with values greater than 75%. However, the addition of 10% biochar resulted in 0% germination. Contaminants were present in the roots of all samples, but they were observed exclusively in the shoots of certain plants. The combination of bioconcentration factor (BCF) < 1 and translocation factor (TF) < 1 suggests mechanisms that limit the uptake of metals and metalloids from the soil, with minimal translocation to the shoots of plants. Regarding ecological risk, improvements were notable with the addition of 10% compost (resulting in lower risks for Cd, Pb, Zn, and Co) and with 5% peat + compost + biochar (resulting in lower risks for Pb, Zn, As, and Ni). The results of ACE and Chao1 for the improvements were equal to or greater than those for soil and slag, indicating the amendments tended to increase species richness. Proteobacteria, Bacteroidota, and Actinobacteriota phyla were identified in the improvements and the presence of amendments altered the soil bacterial community at the genus level. Although peat, compost, and biochar (including their combined use) are promising alternatives for PTMs contaminated soils, the addition rates must be adjusted correctly for avoiding undesirable ecotoxicological effects.
... Soils harbor significant biodiversity with innumerable organisms that interact in complex communities from which critical ecosystem processes emerge (Orgiazzi et al., 2016;Nielsen et al., 2015). Despite this, soils are degrading at an alarming rate globally with persistent threats to soil biodiversity (Orgiazzi et al., 2016;Amundson et al., 2015). ...
... Soils harbor significant biodiversity with innumerable organisms that interact in complex communities from which critical ecosystem processes emerge (Orgiazzi et al., 2016;Nielsen et al., 2015). Despite this, soils are degrading at an alarming rate globally with persistent threats to soil biodiversity (Orgiazzi et al., 2016;Amundson et al., 2015). Soil scientists face challenges like those in climate change discourse when communicating about global soil degradation: the public lacks a nuanced understanding of the problem; it is difficult to translate awareness to action and behavioral change; and the broad scope of the problems (and solutions) may lead to feelings of being overwhelmed and hopeless (Moser, 2016). ...
... Specific key messages can help soil ecologists and disciplinary allies communicate about and advocate for soil biodiversity more effectively. The Global Soil Biodiversity Atlas identifies seven key messages specific to the conservation of soil life including the importance of the soil as habitat, identifying patterns of soil biodiversity around the globe, connecting soil biodiversity with specific ecosystem services, threats to soil biodiversity, and prioritizing policy solutions (Orgiazzi et al., 2016). The editorials we reviewed echo these messages. ...
... O solo também é um dos habitats mais diversos da Terra, abrigando cerca de 59% das espécies existentes no planeta (Anthony et al., 2023). A sua fração orgânica inclui uma densa rede de atividade biológica que mantém processos químicos e biológicos, tais como o armazenamento de carbono, reciclagem de nutrientes e a diversidade de espécies vegetais (Orgiazzi et al., 2016). Esta rede, desempenha um papel fundamental na manutenção da fertilidade do solo, desintoxicação de poluentes, estruturação do solo e regulação da abundância de organismos edáficos (Lavelle, 1997;Ferris et al., 2001). ...
... No seu conjunto, as comunidades de nemátodes, são cruciais para o funcionamento dos ecossistemas terrestres, desempenhando papéis centrais na regulação do ciclo biogeoquímico, dinâmica do carbono, reciclagem de nutrientes, tipo e abundância de vegetação e no controlo das populações de microrganismos do solo (Orgiazzi et al., 2016;Kouser et al., 2021). ...
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RESUMO O solo é um sistema dinâmico e um nicho de biodi-versidade que oferece suporte, refúgio e substrato para diferentes organismos. Quando saudável, o solo sustenta uma elevada biodiversidade, produ-tividade agrícola/florestal e contribui para vários serviços dos ecossistemas. Em solos alterados pelo homem é fundamental monitorizar a sua qualidade como parte de um processo de gestão sustentável. A qualidade do solo engloba as suas características físicas, químicas e biológicas. No século XX, os cientistas começaram a estudar os nemátodes como bioindicadores da qualidade do solo. Embora a comunidade agrícola frequente-mente considere os nemátodes prejudiciais para as culturas, é importante reconhecer o seu papel no equilíbrio do ecossistema do solo. Desta forma, pre-tende-se destacar a relevância das comunidades de nemátodes como indicadores das dinâmicas do solo, assim como o seu papel na manutenção da fertilidade, reciclagem de nutrientes e na supressão de organismos patogénicos que podem desequili-brar o ecossistema do solo.
... Earthworms and enchytraeids support vital soil processes via soil structure modification, consumption of dead organic matter, and interactions with microbial and plant assemblages (Briones, 2014;Conti and Mulder, 2022;Lavelle et al., 2016;Orgiazzi et al., 2016). The study of earthworm and enchytraeid assemblages is relevant because these organisms ensure the quality and functionality of soils and can be used to evaluate soil conditions (Pelosi and Römbke, 2018;Stroud, 2019). ...
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Earthworms and enchytraeids play an important role in biogeochemical cycles and are good indicators of soil fertility. However, assessing their assemblages is difficult, mainly because the methods to identify them require expert knowledge, which becomes a technical challenge when surveying large areas. Soil DNA metabarcoding is a promising method that enables the identification of individual species directly from a bulk composite sample in large field experiments. Here, we investigated in parallel both earthworm (family Lumbricidae) and enchytraeid (family Enchytraeidae) assemblages in three land-use types (arable land, grassland, forest) across 29 Swiss Soil Monitoring Network (NABO) sites, using high-throughput amplicon sequencing of marker genes. For both earthworms and enchytraeids, α-diversity was higher in grasslands than in arable land and forests, and it was significantly affected by soil physico-chemical, climate and biological properties, especially pH and climate properties. In addition, we found negative correlations between earthworms α-diversity and soil total carbon (TC) content and the soil carbon to nitrogen ratio. Using the DNA metabarcoding, we observed sequences of Aporrectodea nocturna in soils with low pH, while other Aporrectodea species occurred in soils with high pH. We identified Bimastos rubidus in soils with low pH but higher TC, total nitrogen, organic C, and low silt content, while the enchytraeids Cognettia sphagnetorum and Cernosvitoviella atrata occurred in forest soils with high water and organic matter contents. We identified some indicator taxa for the different land-use types, for grassland: Aporrectodea icterica, Lumbricus rubellus, Marionina communis, Fridericia bisetosa and Fridericia connata; arable land: Allolobophora chlorotica, Enchytraeus dichaetus, Achaeta iberica, Prodtodrilus antipae and Fridericia tuberosa; and for forest: Octolasion cyaneum, Octolasion lacteum and Cognettia chlorophila. Although these indicator taxa are unlikely to provide information about the effect of land-use change on soil biodiversity at large spatial scales, these species do drive assemblage differences between land-use types. Soil DNA metabarcoding could therefore assist land managers in monitoring soil biodiversity and quality.
... Collembola (Hexapoda: Entognatha) are among the most abundant groups of soil fauna in forest soils (Orgiazzi et al., 2016), with densities that can reach up to 10 5 individuals per m 2 (Petersen and Luxton, 1982). They play an important role in soil food webs and ecosystem processes such as litter decomposition by grazing plant materials and soil fungi and simulating nutrient cycling (Seastedt, 1984;Sackett et al., 2010;Frouz, 2018). ...
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While there is an emerging body of research showing the consequences of land use intensity on soil biodiversity, most studies focus on biodiversity responses to a single or a limited number of agricultural practices in controlled settings or at a single field site, neglecting that multiple practices are simultaneously applied by farmers in real agroecosystems. The combined effects of various agricultural practices have, until now, been largely overlooked in agroecosystems. Here, we conducted a field soil sampling campaign on 87 farms with two land use types (39 arable fields and 48 grasslands) to investigate the relationship between land use intensity, determined by various agricultural practices, and multiple soil communities (bacteria, fungi, protists and invertebrates) at regional scales. We found that land use intensity influenced the diversity and community composition of various soil taxa differently, and these impacts strongly depended on land use type. Soil fungi were most susceptible to land use intensity in both arable fields and grasslands. Specifically, irrigation and pest control were the main practices shaping soil communities in arable fields, while phosphorus and nitrogen fertilization were the main practices structuring soil communities in grasslands. Furthermore, an increase in land use intensity led to greater soil network complexity in arable fields. Our findings reveal regional on-farm patterns of land use intensity effects on various soil communities and identified key agricultural practices that structure soil communities. A key strength of this study is that these patterns can be generalized because the samples were collected from 87 farmlands where multiple agricultural practices were implemented simultaneously. Overall, this work provides a comprehensive perspective on the different responses of multiple soil communities and their associations to land use intensity in agroecosystems.
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Introduction Agriculture is undergoing an agroecological transition characterized by adopting new practices to reduce chemical fertilizer inputs. In this context, digestates are emerging as sustainable substitutes for mineral fertilizers. However, large-scale application of digestates in agricultural fields requires rigorous studies to evaluate their long-term effects on soil microbial communities, which are crucial for ecosystem functioning and resilience. Material and methods This study presents provides a comparative analysis in long-term field conditions of fertilization strategies combining annual applications of raw digestate with biennial applications of different organic waste products (OWPs)—biowaste compost (BIO), farmyard manure (FYM), and urban sewage sludge (SLU)—and compares them to combinations of the same OWPs with mineral fertilizers. The cumulative effects of repeated OWP applications, paired with two nitrogen sources—organic (digestate) and chemical (mineral fertilizer)—were assessed through soil physicochemical and microbial analyses. We hypothesized that the combined effect varied according to the N-supply sources and that this effect also depended on the type of OWP applied. Soil microbial communities were characterized using high-throughput sequencing targeting 16S and 18S ribosomal RNA genes, following DNA extraction from soil samples collected in 2022, six years after the initial digestate application. Results The results indicated that combining OWPs rich in stable and recalcitrant organic matter, such as BIO and FYM, with raw digestate, offers an improved fertilization practice. This approach maintains soil organic carbon (SOC) levels, increases soil phosphorus and potassium content, and stimulates microbial communities differently than nitrogen supplied via mineral fertilizers. While microbial biomass showed no significant variation across treatments, microbial diversity indices exhibited differences based on the type of OWP and nitrogen source. The fertilization strategies moderately influenced prokaryotic and fungal community structures, with distinct patterns depending on the OWP and nitrogen source. Notably, fungal communities responded more strongly to treatment variations than prokaryotic communities. Discussion This study provides new insights into the cumulative effects of substituting mineral fertilizers with digestates on soil microbial communities and soil physicochemical parameters. The sustainable development of agroecosystems significantly depends on a better understanding of the complex responses of soil microbial communities to different fertilization regimes. Future research should continue to assess the long-term impact of digestate application on soil microbiota in real agronomic field conditions, considering associated agricultural practices.
Article
Soils harbor more than half of Earth’s biodiversity, with soil fauna representing one of the most diverse groups. However, understanding the drivers influencing their biodiversity remains limited. Upper Andean tropical forests are among Earth’s most biodiverse ecosystems, but have undergone large-scale historical transformations, resulting in landscapes with different forest successional stages. In this study, we aimed to analyze soil fauna communities along a successional gradient in Colombia’s Eastern Andean forests and identify key microclimatic, soil, and forest structural drivers. We collected soil fauna from 168 samples (30 × 30 × 5 cm), in dry and wet seasons, in 14 permanent plots (20 × 20 m) located in four sites. Data on microclimate, nutrients, productivity, plant diversity, and litter functional richness were gathered from these permanent plots. We observed significant soil fauna biodiversity turnover among Andean montane forest sites, mirroring the distinctive floristic composition between them. We also found that soil fauna richness and abundance increased with succession, attributed to higher productivity and more suitable microclimatic conditions in old-growth forests. Our findings suggest that the primary driver of soil fauna richness in tropical mountain Andean forests is the amount of energy (i.e, forest productivity), while soil fauna abundance is mainly influenced by thermal conditions. Additionally, factors framed within the physiological tolerance hypothesis (i.e., calcium, aluminum) and within the habitat heterogeneity hypothesis (i.e., litter functional richness, plant diversity) also play a role, albeit to a lesser extent. This study emphasizes the importance of examining forest recovery including soil fauna groups to understand successional patterns in tropical mountain forests.
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This is the first taxonomic study of Collembola in Taiwan integrating morphological and molecular evidence to investigate the Taiwanese species in the genus Ptenothrix Börner. We discovered that specimens previously identified as Ptenothrix denticulata (Folsom, 1899) actually consist of several cryptic species, of which we described two species new to science. Our data revealed that, although these species are remarkably similar to each other, they can be distinguished by color patterns, chaetotaxic characters and DNA barcoding (COI). We also designated one of the syntypes of Ptenothrix denticulata (Folsom, 1899) as its lectotype, and treated Dicyrtoma denticulata (Salmon 1964) as a synonym of Ptenothrix denticulata (Salmon 1964) (syn. nov.). Lastly, our study suggests that the diversity of Collembola in Taiwan is still poorly understood, with a high potential for new studies focusing on these microarthropods.
Article
Anaerobic digestion represents an opportunity for converting organic waste (OW) into valuable products: renewable energy (biogas) and a fertilizer (digestate). However, the long-term effects of digestates on soil biota, especially microorganisms, need to be better documented to understand the impact of digestate on soil ecosystem functioning and resilience. This study assessed the cumulative effect of repeated pig slurry digestate applications on soil microbial communities over a decade, using an in-situ approach to compare digested feedstock with undigested feedstock and other fertilization treatments. Conducted from 2012 to 2022 at an experimental field site in France, the study involved plots with identical agricultural soil management practices, differing only in fertilization treatments: mineral fertilizer, three different OW (cattle manure, pig slurry, pig slurry digestate), and a control with no organic or mineral fertilizer input. Changes in soil microbial communities were analyzed through molecular microbial biomass and diversity assessments using high-throughput sequencing targeting 16S and 18S ribosomal RNA genes. DNA extraction and molecular analyses were performed on soil samples collected at the start of the trial in 2012 and subsequently in 2017 and 2022. The long-term effects of annual digestate application over a decade include a higher soil microbial diversity in digestate-treated plots than in pig slurry-treated plots, and changes in the soil's microbial community structure and taxonomic composition resembling those observed with mineral fertilizer. Differential abundance analysis at the phylum level revealed few significant differences between digestate- and mineral fertilizer-treated plots for both prokaryotic and fungal communities. Only plots amended with cattle manure exhibited higher soil organic carbon content. Agricultural practices, along with climatic and environmental fluctuations, can significantly influence the response of soil microbial communities, thereby buffering the effects of fertilization treatments. Further research is needed to better understand the effects on soil microbial communities, considering the interactions between repeated digestate applications, different pedological contexts, and agricultural practices.
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