Joana Falcão Salles

• Professor (Full) at University of Groningen

Farming of houseflies, as well as of other insects, could become a sustainable alternative for producing high-protein animal feed. Although promising, this comes with particular challenges, including monitoring insect health in large-scale farming facilities. In this study, we tested if the expression patterns of immunity-related genes could serve...

Background Gut microbiotas play a pivotal role in host physiology and behaviour, and may affect host life-history traits such as seasonal variation in host phenotypic state. Generally, seasonal gut microbiota variation is attributed to seasonal diet variation. However, seasonal temperature and day length variation may also drive gut microbiota vari...

Microbiomes are involved in most vital processes, such as immune response, detoxification, and digestion and are thereby elementary to organismal functioning and ultimately the host’s fitness. In turn, the microbiome may be influenced by the host and by the host’s environment. To understand microbiome dynamics during the process of adaptation to ne...

Coenzyme A (CoA) is essential for metabolism and protein acetylation. Current knowledge holds that each cell obtains CoA exclusively through biosynthesis via the canonical five-step pathway, starting with pantothenate uptake. However, recent studies have suggested the presence of additional CoA-generating mechanisms, indicating a more complex syste...

Rearing insects for food and feed is a rapidly growing industry, because it provides excellent opportunities for a sustainable approach to animal protein production. Two fly species, the black soldier fly (BSF) and the house fly (HF), naturally live in decaying organic matter (e.g. compost), and can thus be effectively reared on organic rest stream...

The digestive tract of animals harbors microbiota important for the host’s fitness and performance. The interaction between digestive tract bacteria and soil animal hosts is still poorly explored despite the importance of soil fauna for ecosystem processes. In this study, we investigated the interactions between the bacterial communities from the d...

Background Inflammation is considered a key factor in the development of postoperative cognitive dysfunction (POCD). Therefore, we hypothesized that pre-operative anti-inflammatory treatment with ibuprofen would inhibit POCD in our rat-model. Methods Male Wistar rats of 3 or 23 months old received a single injection of ibuprofen (15 mg/kg i.p.) or...

Soil microbiome manipulation can potentially reduce the use of pesticides by improving the ability of soils to resist or recover from pathogen infestation, thus generating natural suppressiveness. We simulated disturbance through soil fumigation and investigated how the subsequent application of bio-organic and organic amendments reshapes the taxon...

Diversity and community structure of soil microorganisms are increasingly recognized as important contributors to sustainable agriculture and plant health. In viticulture, grapevine scion cultivars are grafted onto rootstocks to reduce the incidence of the grapevine pest phylloxera. However, it is unknown to what extent this practice influences roo...

Plant-associated bacterial communities are important contributors towards plant health and productivity, and are increasingly acknowledged for having the potential to alter plants' response to climate extremes, such as drought. Viticulture is generally conducted in areas that are prone to seasonal water deficit, and irrigation is the common way to...

Classical ecological theory posits that species partition resources such that each species occupies a unique resource niche. In general, the availability of more resources allows more species to co‐occur. Thus, a strong relationship between communities of consumers and their resources is expected. However, correlations may be influenced by other la...

To understand how and to what extent single or multiple perturbations can alter the relationships between the abundances of different nitrifier groups and nitrification, soil microcosms were exposed to six disturbance treatments: a heat shock, cold shock, or control conditions applied to undisturbed soils or to soils that had previously been subjec...

Elytrigia atherica is a native invasive plant species whose expansion on salt marshes is attributed to genotypic and phenotypic adaptations to non-ideal environmental conditions, forming two ecotypes. It is unknown how E. atherica–microbiome interactions are contributing to its adaptation. Here we investigated the effect of sea-water flooding frequ...

Classical ecological theory posits that species partition resources such that each species occupies a unique resource niche. In general, the availability of more resources allows more species to co‐occur. Thus, a strong relationship between communities of consumers and their resources is expected. However, correlations may be influenced by other la...

Ecological theory suggests that a combination of local and regional factors regulate biodiversity and community functioning in metacommunities. The relative importance of different factors structuring communities likely changes over successional time, but to date this concept is scarcely documented. In addition, the few studies describing successio...

Background The relevance of the host microbiota to host ecology and evolution is well acknowledged. However, the effect of the microbial environment on host immune function and host microbiota dynamics is understudied in terrestrial vertebrates. Using a novel experimental approach centered on the manipulation of the microbial environment of zebra f...

In the context of food safety, edible insects are evaluated for biological hazards such as microbial pathogens according to regulations currently in place. When the European Food Safety Authority evaluated the hazards of edible insects as a potential source of pathogenic viruses for humans and livestock, the novel zoonotic coronavirus SARS-CoV-2 ha...

Non-target effects of deliberately releasing organisms into a new environment are of great concern due to their potential impact on the biodiversity and functioning of ecosystems. Whereas these studies often focus on invasive species of macro-organisms, the use of microbial inoculants is often expected to have specific effects on particular functio...

Quantifying which assembly processes structure microbiomes can assist prediction, manipulation, and engineering of community outcomes. However, the relative importance of these processes might depend on whether DNA or RNA are used, as they differ in stability. We hypothesized that RNA-inferred community responses to (a)biotic fluctuations are faste...

Microbiomes and their hosts influence each other; for instance, the microbiome improves host fitness, whereas the host supports microbiome nutrition. Most studies on this topic have focused on the role of bacteria and fungi, although research on viruses that infect bacteria, known as ‘bacteriophages’ (phages), has gained importance due to the poten...

Soil microbial communities are often not resistant to the impact caused by microbial invasions, both in terms of structure and functionality, but it remains unclear whether these changes persist over time. Here we used 3 strains of Escherichia coli O157:H7 (E. coli O157:H7), a species used for modelling bacterial invasions, to evaluate the resilien...

Terrestrial plants establish symbiosis with arbuscular mycorrhizal fungi (AMF) to exchange water and nutrients. However, the extent to which soil biodiversity influences such association remains still unclear. Here, we manipulated the soil microbial diversity using a “dilution-to-extinction” approach in a controlled pot microcosm system and quantif...

Two bacterial strains, denoted so4 and w15, isolated from wheat straw (WS)-degrading microbial consortia, were found to grow synergistically in media containing WS as the single carbon and energy source. They were identified as Citrobacter freundii so4 and Sphingobacterium multivorum w15 based on 16S rRNA gene sequencing and comparison to the respe...

Microorganisms play a crucial role in lignocellulosic degradation. Many enriched microbial communities have demonstrated to reach functional and structural stability with effective degrading capacities of industrial interest. These microbial communities are typically composed by only few dominant species and a high number of usually overlooked rare...

Vertebrates evolved in concert with bacteria and have developed essential mutualistic relationships. Gut bacteria are vital for the postnatal development of most organs and the immune and metabolic systems and may likewise play a role during prenatal development. Prenatal transfer of gut bacteria is shown in four mammalian species, including humans...

Ethyl tert-butyl ether (ETBE) is a gasoline additive that became an important aquifer pollutant. The information about natural bacterial consortia with a capacity for complete ETBE degradation is limited. Here we assess the taxonomical composition of bacterial communities and diversity of the ethB gene (involved in ETBE biodegradation) in ETBE-enri...

With no efficient method widely recognized for controlling or preventing tomato bacterial wilt, a devastating disease caused by the soil-borne bacterium Ralstonia solanacearum, tomato production is severely hindered. Therefore, the objective was thus to provide a strategy based on fumigation using ammonium bicarbonate along with organic amendment t...

During the last decades it has become increasingly clear that the microbes that live on and in humans are critical for health. The communities they form, termed microbiomes, are involved in fundamental processes such as the maturation and constant regulation of the immune system. Additionally, they constitute a strong defense barrier to invading pa...

When studying the effects of climate change on eukaryotic organisms we often oversee a major ecological process: the interaction with microbes. Eukaryotic hosts and microbes form functional units, termed holobionts, where microbes play crucial roles in host functioning. Environmental stress may disturb these complex mutualistic relations. Macroalga...

Symbiosis between microbial associates and a host is a ubiquitous feature of life on earth, modulating host phenotypes. In addition to endosymbionts, organisms harbour a collection of host-associated microbes, the microbiome that can impact important host traits. In this opinion article we argue that the mutual influ- ences of the microbiome and en...

Insects are associated with multiple microbes that have been reported to influence various aspects of their biology. Most studies in insects, including pest species, focus on the bacterial communities of the microbiome even though the microbiome consists of members of many more kingdoms, which can also have large influence on the life history of in...

The soil environment teems with microbes that play fundamental roles in controlling biogeochemical cycles, thus providing support for organisms above and below ground to thrive. With the contemporary development of high-throughput DNA sequencing technologies, a growing body of literature has shown that organismal composition and abundance within mi...

Disentangling the relative influences of soil properties and plant-host on root-associated microbiomes in natural systems is challenging, given that spatially segregated soil types display distinct historical legacies. In addition, distant locations may also lead to biogeographical patterns of microbial communities. Here, we used an undisturbed sal...

The soil microbiome is a complex living network that plays essential roles in agricultural systems, regardless of the level of intensification. However, the effects of agricultural management on the soil microbiome and the association with plant productivity remain largely unclear. Here, we studied the responses of three soil systems displaying dis...

Enriched microbial communities, obtained from environmental samples through selective processes, can effectively contribute to lignocellulose degradation. Unfortunately, fully controlled industrial degradation processes are difficult to reach given the intrinsically dynamic nature and complexity of the microbial communities, composed of a large num...

Ancestor microbes started colonizing inland habitats approximately 2.7 to 3.5 billion years ago. With some exceptions, the key physiological adaptations of microbiomes associated with marine-to-land transitions have remained elusive. This is essentially caused by the lack of suitable systems that depict changes in microbiomes across sufficiently la...

Acclimatization via changes in the stable (core) or the variable microbial diversity and/or abundance is an important element in the adaptation of coral species to environmental changes. Here, we explored the spatial-temporal dynamics, diversity and interactions of variable and core bacterial populations associated with the coral Mussismilia hispid...

Venn diagram displaying the degree of overlap of bacterial OTUs between the site-stable bacterial populations (persistent OTUs found within each reef/sampling point) from bacteriomes of Reefs 1, 3, and 5. The vertically transferred core bacteriome members (Leite et al., 2017) are highlighted.

Non-metric multidimensional scaling (NMS) based on the quantitative values of the matrix profiles of the PCR-DGGE profile for the seawater bacterial communities in the rainy (A,B) and dry (C,D) seasons (n = 4).

Non-metric multidimensional scaling based on the quantitative values of the matrix profiles of the PCR-DGGE profile for the bacterial communities associated with the coral Mussismilia hispida in the rainy (A,B) and dry (C,D) seasons (n = 4).

Rarefaction curves from bacterial communities of M. hispida (considering OTU level) at different sampling locations (R1, R3, and R5) and over time (rainy and dry seasons).

Environmental conditions at the sampling locations (n = 4).

Scheme demonstrating the experimental strategy used in this study. The horizontal arrow indicates the timeline. The vertical arrow in gray indicates the river’s influence on the reefs.

(A) Principal coordinates analysis (PCoA) (weighted UniFrac) based on the distance matrix for operational taxonomic units (OTUs), showing differences between seawater and M. hispida bacteriomes (PERMANOVA, pseudo-F: 204.47, p < 0.001), and (B) Richness of seawater and M. hispida bacteriome based on phylogenetic distance (Tukey test, p < 0.001).

(A) Absolute (mean standard deviation) abundance of Enterobacteriaceae (represented by three different OTUs) in M. hispida bacteriomes at different sampling locations (R1, R3, and R5) (n = 4). Different letters indicate significant difference between samples (Mann–Whitney test, p < 0.05). (B) Correlation plot showing the functional correlation betw...

Background Inflammation is considered a key factor in the development of post‐operative cognitive dysfunction (POCD). We hypothesize that acute preoperative anti‐inflammatory treatment with ibuprofen improves postoperative cognitive performance involving the gut‐brain axis in a rat‐model of POCD. Methods Male Wistar rats of 3 and 23 months old wer...

The microbial degradation of plant-derived compounds under salinity stress remains largely underexplored. The pretreatment of lignocellulose material, which is often needed to improve the production of lignocellulose monomers, leads to high salt levels, generating a saline environment that raises technical considerations that influence subsequent d...

Our planet teems with microorganisms that often present a skewed abundance distribution in a local community, with relatively few dominant species coexisting alongside a high number of rare species. Recent studies have demonstrated that these rare taxa serve as limitless reservoirs of genetic diversity, and perform disproportionate types of functio...

Plant biomass (PB) is an important source of sugars useful for biofuel production, whose degradation efficiency depends on synergistic and dynamic interactions of different enzymes. Here, using a metatranscriptomics-based approach, we explored the expression of PB-degrading enzymes in a five-species synthetic bacterial consortium during cultivation...

The microbiome is essential for development, health and homeostasis throughout an animal's life. Yet, the origins and transmission processes governing animal microbiomes remain elusive for non-human vertebrates, oviparous vertebrates in particular. Eggs may function as transgenerational carriers of the maternal microbiome, warranting characterisati...

Soil microbial communities have remarkable capacities to cope with ceaseless environmental changes, but little is known about their adaptation potential when facing an unprecedented disturbance. We tested the effect of incremental dose of microwaving on soil bacteria as a model of unprecedented stress. 16S rRNA gene qPCR at both the DNA and cDNA le...

Although many environments like soils are constantly subjected to invasion by alien microbes, invaders usually fail to succeed, succumbing to the robust diversity often found in nature. So far, only successful invasions have been explored, and it remains unknown to what extent an unsuccessful invasion can impact resident communities. Here we hypoth...

Despite the importance of coral microbiomes for holobiont persistence, the interactions among these are not well understood. In particular, knowledge of the co-occurrence and taxonomic importance of specific members of the microbial core, as well as patterns of specific mobile genetic elements (MGEs), is lacking. We used seawater and mucus samples...

Background: Working toward a general framework to understand the role of microbiota in animal biology requires the characterisation of animal-associated microbial communities and identification of the evolutionary and ecological factors shaping their variation. In this study, we described the microbiota in the cloaca, brood patch skin and feathers...

Considering the great agronomic and environmental importance of denitrification, the aim of the present study was to study the temporal and spatial factors controlling the abundance and activity of denitrifying bacterial communities in a range of eight agricultural soils over 2 years. Abundance was quantified by qPCR of the nirS, nirK and nosZ gene...

Plant-associated bacteria are known for their high functional trait diversity, from which many are likely to play a role in primary and secondary succession, facilitating plant establishment in suboptimal soils conditions. Here we used an undisturbed salt marsh chronosequence that represents over 100 years of soil development to assess how the func...

Recent research suggests that prior exposure of several months to elevated irradiance induces enhanced thermal tolerance in scleractinian corals. While this tolerance has been reported at the species level, individual coral colonies may react differently due to individual variability in thermal tolerance. As thermal anomalies are predicted to becom...

Figure S1: Image of light spectrum. Spectrum of Orphek PR-156W.

Table S2: Table displaying significant main effects and interactions (excluding colony). Summary of significant main effects and interactions based on factorial analysis of variance for photographic analyses and fluorescence (EQY).

Figure S2: Image of each group of ramets after fragging and during heat stress. Photographs of Stylophora pistillata ramet (one ramet per group) after fragging, and during heat stress (day 44, 51 and 57). Control treatment (CT). Experimental treatment (ET). Colony 1 (C1), Colony 2 (C2) and Colony 3 (C3).

Figure S3: Image of DGGE gel (Symbiodinium ITS2). DGGE gel displaying Symbiodinium community based on ITS2.

Table S1: Table displaying significant main effects and interactions (including colony). Summary of significant main effects and interactions based on factorial analysis of variance for specific growth rate (during light treatment), cell density, chlorophyll a and photographic analyses, linear mixed model for fluorescence (EQY) and permutational mu...

Lignocellulosic biomass (LCB) is an attractive source of carbon for the production of sugars and other chemicals. Due to its inherent complexity and heterogeneity, efficient biodegradation requires the actions of different types of hydrolytic enzymes. In nature, complex microbial communities that work efficiently and often synergistically accomplis...

Increasing climatic and anthropogenic pressures on soil ecosystems are expected to create a global patchwork of disturbance scenarios. Some regions will be strongly impacted by climate change, others by agricultural intensification, and others by both. Soil microbial communities are integral components of terrestrial ecosystems, but their responses...

The type and frequency of disturbances experienced by soil microbiomes is expected to increase given predicted global climate change scenarios and intensified anthropogenic pressures on ecosystems. While the direct effect of multiple disturbances to soil microbes has been explored in terms of function, their effect on the recovery of microbial comm...