Search

Metabarcoding of DNA extracted from environmental or bulk specimen samples is increasingly used to profile biota in basic and applied biodiversity research because of its targeted nature that allows sequencing of genetic markers from many samples in parallel. To achieve this, PCR amplification is carried out with primers designed to target a taxonomically informative marker within a taxonomic group, and sample-specific nucleotide identifiers are added to the amplicons prior to sequencing. The latter enables assignment of the sequences back to the samples they originated from. Nucleotide identifiers can be added during the metabarcoding PCR and during "library preparation", that is, when amplicons are prepared for sequencing. Different strategies to achieve this labelling exist. All have advantages, challenges and limitations, some of which can lead to misleading results, and in the worst case compromise the fidelity of the metabarcoding data. Given the range of questions addressed using metabarcoding, ensuring that data generation is robust and fit for the chosen purpose is critically important for practitioners seeking to employ metabarcoding for biodiversity assessments. Here, we present an overview of the three main workflows for sample-specific labelling and library preparation in metabarcoding studies on Illumina sequencing platforms; one-step PCR, two-step PCR, and tagged PCR. Further, we distill the key considerations for researchers seeking to select an appropriate metabarcoding strategy for their specific study. Ultimately, by gaining insights into the consequences of different metabarcoding workflows, we hope to further consolidate the power of metabarcoding as a tool to assess biodiversity across a range of applications., Molecular Ecology Resources, 22 (4), ISSN:1755-098X, ISSN:1471-8278, ISSN:1755-0998, ISSN:1471-8286

International audience; The impact of glacier retreat on fungal-driven decomposition in rivers is investigated using a standardized test across six countries. Less glacier cover is linked to increased decomposition, which is in turn associated with a greater abundance of fungi and a fungal cellulose-degrading gene, cbhI.Climate change is altering the structure and functioning of river ecosystems worldwide. In mountain rivers, glacier retreat has been shown to result in systematic changes in aquatic invertebrate biodiversity, but the effects of ice loss on other biological taxa and on whole-ecosystem functions are less well understood. Using data from mountain rivers spanning six countries on four continents, we show that decreasing glacier cover leads to consistent fungal-driven increases in the decomposition rate of cellulose, the world's most abundant organic polymer. Cellulose decomposition rates were associated with greater abundance of aquatic fungi and the fungal cellulose-degrading Cellobiohydrolase I (cbhI) gene, illustrating the potential for predicting ecosystem-level functions from gene-level data. Clear associations between fungal genes, populations and communities and ecosystem functioning in mountain rivers indicate that ongoing global decreases in glacier cover can be expected to change vital ecosystem functions, including carbon cycle processes.

Aim Ecological communities that exist closer together in space are generally more compositionally similar than those far apart, as defined by the distance?decay of similarity relationship. However, recent research has revealed substantial variability in the distance?decay relationships of microbial communities between studies of different taxonomic groups, ecosystems and spatial scales and between those using different molecular methodologies (e.g., high-throughput sequencing versus molecular fingerprinting). Here, we test how these factors influence the strength of microbial distance?decay relationships, in order to draw generalizations about how microbial ?-diversity scales with space. Location Global. Time period Studies published between 2005 and 2019 (inclusive). Major taxa studied Bacteria, Archaea and microbial Eukarya. Methods We conducted a meta-analysis of microbial distance?decay relationships, using the Mantel correlation coefficient as a measure of the strength of distance?decay relationships. Our final dataset consisted of 452 data points, varying in environmental/ecological context or methodological approaches, and we used linear models to test the effects of each variable. Results Both ecological and methodological factors had significant impacts on the strength of microbial distance?decay relationships. Specifically, the strength of these relationships varied between environments and habitats, with soils showing significantly weaker distance?decay relationships than other habitats, whereas increasing spatial extents had no effect. Methodological factors, such as sequencing depth, were positively related to the strength of distance?decay relationships, and choice of dissimilarity metric was also important, with phylogenetic metrics generally giving weaker distance?decay relationships than binary or abundance-based indices. Main conclusions We conclude that widely studied microbial biogeographical patterns, such as the distance?decay relationship, vary by ecological context but are primarily distorted by methodological choices. Consequently, we suggest that by linking methodological approaches appropriately to the ecological context of a study, we can progress towards generalizable biogeographical relationships in microbial ecology.

Aims Saprophytic fungi are important agents of soil mineralization and carbon cycling. Their community structure is known to be affected by soil conditions such as organic matter and pH. However, the effect of plant species, whose roots provide the litter input into the soil, on the saprophytic fungal community is largely unknown. Methods We examined the saprophytic fungi in a grassland biodiversity experiment with eight plant species belonging to two functional groups (grasses and forbs), combining DNA extraction from plant roots, next-generation sequencing and literature research. Results We found that saprophyte richness increased with plant species richness, but plant functional group richness was the best predictor. Plant functional group was also the main factor driving fungal saprophytic community structure. This effect was correlated with differences in root lignin content and C:N ratio between grasses and forbs. In monocultures, root traits and plant functional group type explained 16% of the variation in community structure. The saprophyte taxa detected in mixed plant communities were to a large extent subsets of those found in monocultures. Conclusions Our work shows that the richness and community structure of the root-associated saprophytic fungi can largely be predicted by plant functional groups and their associated root traits. This means that the effects of plant diversity on ecosystem functions such as litter decomposition may also be predictable using information on plant functional groups in grasslands.

Scientists and practitioners working on river restoration have made progress on understanding the recovery potential of rivers from geomorphological and engineering perspectives. We now need to build on this work to gain a better understanding of the biological processes involved in river restoration. Environmental policy agendas are focusing on nature recovery, reigniting debates about the use of “natural” reference conditions as benchmarks for ecosystem restoration. We argue that the search for natural or semi-natural analogues to guide restoration planning is inappropriate due to the absence of contemporary reference conditions. With a catchment-scale case study on the invertebrate communities of the Warwickshire Avon, a fifth-order river system in England, we demonstrate an alternative to the reference condition approach. Under our model, recovery potential is quantified based on the gap between observed biodiversity at a site and the biodiversity predicted to occur in that location under alternative management scenarios. We predict that commonly applied restoration measures such as reduced nutrient inputs and the removal of channel resectioning could be detrimental to invertebrate diversity, if applied indiscriminately and without other complementary measures. Instead, our results suggest considerable potential for increases in biodiversity when restoration measures are combined in a way that maximises biodiversity within each water body.

Centrate is a low-cost alternative to synthetic fertilizers for microalgal cultivation, reducing environmental burdens and remediation costs. Adapted microalgae need to be selected and characterised to maximise biomass production and depuration efficiency. Here, the performance and composition of six microalgal communities cultivated both on synthetic media and centrate within semi-open tubular photobioreactors were investigated through Illumina sequencing. Biomass grown on centrate, exposed to a high concentration of ammonium, showed a higher quantity of nitrogen (5.6% dry weight) than the biomass grown on the synthetic media nitrate (3.9% dry weight). Eukaryotic inocula were replaced by other microalgae while cyanobacterial inocula were maintained. Communities were generally similar for the same inoculum between media, however, inoculation with cyanobacteria led to variability within the eukaryotic community. Where communities differed, centrate resulted in a higher richness and diversity. The higher nitrogen of centrate possibly led to higher abundance of genes coding for N metabolism enzymes.

The ecological impacts of long-term elevated atmospheric CO2 (eCO2 ) levels on soil microbiota remain largely unknown. This is particularly true for the arbuscular mycorrhizal (AM) fungi, which form mutualistic associations with over two-thirds of terrestrial plant species and are entirely dependent on their plant hosts for carbon. Here, we use high-resolution amplicon sequencing (Illumina, HiSeq) to quantify the response of AM fungal communities to the longest running (>15 years) free-air carbon dioxide enrichment (FACE) experiment in the Northern Hemisphere (GiFACE); providing the first evaluation of these responses from old-growth (>100 years) semi-natural grasslands subjected to a 20% increase in atmospheric CO2 . eCO2 significantly increased AM fungal richness but had a less-pronounced impact on the composition of their communities. However, while broader changes in community composition were not observed, more subtle responses of specific AM fungal taxa were with populations both increasing and decreasing in abundance in response to eCO2 . Most population-level responses to eCO2 were not consistent through time, with a significant interaction between sampling time and eCO2 treatment being observed. This suggests that the temporal dynamics of AM fungal populations may be disturbed by anthropogenic stressors. As AM fungi are functionally differentiated, with different taxa providing different benefits to host plants, changes in population densities in response to eCO2 may significantly impact terrestrial plant communities and their productivity. Thus, predictions regarding future terrestrial ecosystems must consider changes both aboveground and belowground, but avoid relying on broad-scale community-level responses of soil microbes observed on single occasions.

Bioaerosols (or biogenic aerosols) have largely been overlooked by molecular ecologists. However, this is rapidly changing as bioaerosols play key roles in public health, environmental chemistry and the dispersal ecology of microbes. Due to the low environmental concentrations of bioaerosols, collecting sufficient biomass for molecular methods is challenging. Currently, no standardized methods for bioaerosol collection for molecular ecology research exist. Each study requires a process of optimization, which greatly slows the advance of bioaerosol science. Here, we evaluated air filtration and liquid impingement for bioaerosol sampling across a range of environmental conditions. We also investigated the effect of sampling matrices, sample concentration strategies and sampling duration on DNA yield. Air filtration using polycarbonate filters gave the highest recovery, but due to the faster sampling rates possible with impingement, we recommend this method for fine ‐scale temporal/spatial ecological studies. To prevent bias for the recovery of Gram‐positive bacteria, we found that the matrix for impingement should be phosphate‐buffered saline. The optimal method for bioaerosol concentration from the liquid matrix was centrifugation. However, we also present a method using syringe filters for rapid in‐field recovery of bioaerosols from impingement samples, without compromising microbial diversity for high ‐throughput sequencing approaches. Finally, we provide a resource that enables molecular ecologists to select the most appropriate sampling strategy for their specific research question.

Continuing losses of multi-year sea ice (MYI) across the Arctic are causing first-year sea ice (FYI) to dominate the Arctic ice pack. Melting FYI provides a strong seasonal pulse of dissolved organic matter (DOM) into surface waters; however, the biological impact of this DOM input is unknown. Here we show that DOM additions cause important and contrasting changes in under-ice bacterioplankton abundance, production and species composition. Utilization of DOM was influenced by molecular size, with 10–100 kDa and >100 kDa DOM fractions promoting rapid growth of particular taxa, while uptake of sulfur and nitrogen-rich low molecular weight organic compounds shifted bacterial community composition. These results demonstrate the ecological impacts of DOM released from melting FYI, with wide-ranging consequences for the cycling of organic matter across regions of the Arctic Ocean transitioning from multi-year to seasonal sea ice as the climate continues to warm. Arctic sea-ice melt causes a release of dissolved organic material (DOM) into the surface waters. The increased dominance of first-year ice and DOM release is impacting under-ice bacterial communities.

The composition and structure of plant-root-associated fungal communities are determined by local abiotic and biotic conditions. However, the relative influence and identity of relationships to abiotic and biotic factors may differ across environmental and ecological contexts, and fungal functional groups. Thus, understanding which aspects of root-associated fungal community ecology generalise across contexts is the first step towards a more predictive framework. We investigated how the relative importance of biotic and abiotic factors scale across environmental and ecological contexts using high-throughput sequencing (ca. 55 M Illumina metabarcoding sequences) of >260 plant-root-associated fungal communities from six UK salt marshes across two geographic regions (South-East and North-West England) in winter and summer. Levels of root-associated fungal diversity were comparable with forests and temperate grasslands, quadrupling previous estimates of salt-marsh fungal diversity. Whilst abiotic variables were generally most important, a range of site- and spatial scale-specific abiotic and biotic drivers of diversity and community composition were observed. Consequently, predictive models of diversity trained on one site, extrapolated poorly to others. Fungal taxa from the same functional groups responded similarly to the specific drivers of diversity and composition. Thus site, spatial scale and functional group are key factors that, if accounted for, may lead to a more predictive understanding of fungal community ecology.

In previous studies eDNA metabarcoding has been demonstrated as a viable tool for catchment-level biodiversity sampling in rivers (Deiner et al. 2016). However, questions still remain over the appropriate sampling protocol for large spatial scale sampling. River reaches are composed of multiple habitats with species composition varying from one to the next (Costa and Melo 2007). Therefore, how many spatial replicates are needed to reliably represent the river network? Is the previously used approach to sample at every river confluence (Deiner et al. 2016) sufficient or is more needed? These questions were addressed using a case study in the headwaters of the Cound Brook, a tributary to the River Severn in Shropshire, UK. Two sub-catchments of the Cound Brook were used. One sub-catchment had a sample taken at the most downstream point before the confluence. Additionally, a sample at the upstream extent of the same sub-catchment was taken to estimate any correlation between the species found at the beginning of the river reach and at the end. Another sub-catchment also had the same up- and downstream sample design. However, in between was a systemic sampling regime every 500 m. This is to test if increasing the spatial resolution gave significantly different results to the sparser sampling regime. At each sample location, a 1 L water sample was sequentially filtered through membranes of three different mesh sizes: 5µm, 0.45µm and 0.2µm. Sequential filtering was performed because DNA resides in two forms in the environment (Civade et al. 2017), within whole cells (cellular DNA) and outside of cells (extracellular). The theory is that the coarser filters predominantly collect cellular DNA and the finer filters collect predominantly extracellular DNA of increasingly smaller fragment lengths. Consequently, sequential filtering could represent DNA degradation in the environment (Fig. 1). Also, Turner et al. 2014 suggested that the larger particles could determine very recent or local organisms. Therefore, we hypothesised that the DNA collected by the coarser filters would represent local diversity and the DNA collected by the finer filters would reflect biodiversity further upstream. Initial results suggest sequential filtering through the 5µm and 0.45µm filters caught detectable levels of eDNA where the 0.2µm did not catch enough to show up through gel electrophoresis. The relevance of the initial finding suggests that if we only used a 5µm filter the data collected at 0.45µm could have been discarded. Further investigations of any differences in species compositions between filters and the relationships to other sampling locations is still to be determined. This ongoing research is intended to determine the appropriate sampling protocol for a large-scale biodiversity assessment regime combining eDNA metabarcoding and species distribution modelling.

Pure microalgae cultivation in organic wastes may be hampered by their low adaptation to extreme growth conditions and by the risk of microbial contamination. This work aimed to isolate self-adapted microalgae-microbial consortia able to survive in organic wastes characterized by extreme conditions, to be then proposed for technological application in removing carbon and nutrients from wastes’ streams. To do so, sixteen organic wastes with different origins and consistency were sampled. Twelve microbial consortia were isolated from wastes and their eukaryotic and prokaryotic compositions were analyzed by next generation sequencing. Eight eukaryotic communities were dominated by Chlorophyta, led by Chlorella, able to survive in different wastes regardless of chemical-biological properties. Tetradesmus, the second most represented genus, grew preferentially in substrates with less stressing chemical-physical parameters. Chlorella and Tetradesmus were mostly isolated from cow slurry and derived wastes which proved to be the best local residual organic source.

Particle size is a significant factor in determining the dispersal and inhalation risk from bioaerosols. Green-waste composting is a significant source of bioaerosols (including pathogens), but little is known about the distribution of specific taxa across size fractions. To characterise size fractionated bioaerosol emissions from a compost facility, we used a Spectral Intensity Bioaerosol Sensor (SIBS) to quantify total bioaerosols and qPCR and metabarcoding to quantify microbial bioaerosols. Overall, sub-micron bioaerosols predominated, but molecular analysis showed that most (>75%) of the airborne microorganisms were associated with the larger size fractions (>3.3 µm da). The microbial taxa varied significantly by size, with Bacilli dominating the larger, and Actinobacteria the smaller, size fractions. The human pathogen Aspergillus fumigatus dominated the intermediate size fractions (>50% da 1.1–4.7 µm), indicating that it has the potential to disperse widely and once inhaled may penetrate deep into the respiratory system. The abundance of Actinobacteria (>60% at da

The most remarkable feature of our planet is the diversity of its life forms, ranging from viruses and nanobacteria to blue whales and giant sequoias to satanic leaf‐tailed geckos and leafy seadragons (look them up!). Life is found in essentially all environments on earth, and the number of species living on our planet is many times greater than we could have imagined a century ago. A well‐regarded estimate pegs the number of eukaryotic species on earth at 8.7 million (±1.3 million), of which fewer than 15% are currently described (Mora et al., 2011). The diversity of prokaryotes is less clear (and highly controversial), but an analysis of 1.6 billion 16S ribosomal RNA sequences estimated that 0.8–1.6 million prokaryotic operational taxonomic units exist globally (Louca et al., 2019). While we do not know how many species are currently extant, or have existed in the past, we do know that this biodiversity is valuable, providing food, fibre and medicine, furnishing ecosystem services such as water and air purification, nutrient cycling, pollination and carbon uptake, and contributing to technological innovations ranging from biotechnology to robotics to material science. Moreover, biodiversity underlies the cultural identity of human populations and is important to human health and well‐being. Geographically, species richness increases from the Polar Regions to the tropics in terrestrial and surface marine ecosystems. Thus, some countries, especially those in tropical and subtropical regions, are endowed with much greater biodiversity than others. Unfortunately, benefits arising from the access and utilization of this biodiversity have been unequally shared, with (paradoxically) biodiversity‐poor countries often accruing the lion's share of economic gains. There can be imbalances within countries as well, wherein some segments of the population obtain greater economic benefits from biodiversity and associated traditional knowledge than indigenous peoples. The “Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization,” which came into force in 2014, is an international agreement designed to ensure that the benefits arising from biodiversity are shared equitably (https://www.cbd.int/abs/). However, few scientific journals require compliance with the Nagoya Protocol or the reporting of benefits from biodiversity research. In this editorial, we (the editors of Molecular Ecology and Molecular Ecology Resources) express support for the Nagoya Protocol and the principle of benefit sharing. We believe that scientific journals publishing research on biodiversity can play an important role in implementing the Nagoya Protocol and in reporting on benefits generated from such research. Below, we provide background on the Nagoya Protocol, discuss the kinds of benefits that may arise from biodiversity research, describe the rationale for reporting on these benefits and introduce changes to the journals’ Data Accessibility Statements to incorporate the requirements and goals of the Nagoya Protocol.

Net emissions of the potent GHG methane from ecosystems represent the balance between microbial methane production (methanogenesis) and oxidation (methanotrophy), each with different sensitivities to temperature. How this balance will be altered by long-term global warming, especially in freshwaters that are major methane sources, remains unknown. Here we show that the experimental warming of artificial ponds over 11 years drives a disproportionate increase in methanogenesis over methanotrophy that increases the warming potential of the gases they emit. The increased methane emissions far exceed temperature-based predictions, driven by shifts in the methanogen community under warming, while the methanotroph community was conserved. Our experimentally induced increase in methane emissions from artificial ponds is, in part, reflected globally as a disproportionate increase in the capacity of naturally warmer ecosystems to emit more methane. Our findings indicate that as Earth warms, natural ecosystems will emit disproportionately more methane in a positive feedback warming loop.\ud \ud

In grasslands, N mineralization and nitrification are important processes and are controlled by several factors, including the in situ microbial community composition. Nitrification involves ammonia oxidising archaea (AOA) and bacteria (AOB) and although AOA and AOB co-exist in soils, they respond differently to environmental characteristics and there is evidence of AOA/AOB niche differentiation. Here, we investigated temporal variation in N mineralization and nitrification rates, together with bacterial, archaeal and ammonia-oxidiser communities in grassland soils, on different geologies: clay, Greensand and Chalk. Across geologies, N mineralization and nitrification rates were slower in the autumn than the rest of the year. Turnover times for soil ammonium pools were

International audience; Classical biomonitoring techniques have focused primarily on measures linked to various biodiversity metrics and indicator species. Next-generation biomonitoring (NGB) describes a suite of tools and approaches that allow the examination of a broader spectrum of organizational levels-from genes to entire ecosystems. Here, we frame 10 key questions that we envisage will drive the field of NGB over the next decade. While not exhaustive, this list covers most of the key challenges facing NGB, and provides the basis of the next steps for research and implementation in this field. These questions have been grouped into current- and outlook-related categories, corresponding to the organization of this paper.

Conversion of tropical forest to agriculture results in reduced habitat heterogeneity, and associated declines in biodiversity and ecosystem functions. Management strategies to increase biodiversity in agricultural landscapes have therefore often focused on increasing habitat complexity; however, the large-scale, long-term ecological experiments that are needed to test the effects of these strategies are rare in tropical systems. Oil palm (Elaeis guineensis Jacq.)—one of the most widespread and important tropical crops—offers substantial potential for developing wildlife-friendly management strategies because of its long rotation cycles and tree-like structure. Although there is awareness of the need to increase sustainability, practical options for how best to manage oil palm plantations, for benefits to both the environment and crop productivity, have received little research attention. In this paper we introduce the Biodiversity and Ecosystem Function in Tropical Agriculture (BEFTA) Programme: a long-term research collaboration between academia and industry in Sumatra, Indonesia. The BEFTA Programme aims to better understand the oil palm agroecosystem and test sustainability strategies. We hypothesise that adjustments to oil palm management could increase structural complexity, stabilise microclimate, and reduce reliance on chemical inputs, thereby helping to improve levels of biodiversity and ecosystem functions. The Programme has established four major components: (1) assessing variability within the plantation under business-as-usual conditions; (2) the BEFTA Understory Vegetation Project, which tests the effects of varying herbicide regimes; (3) the Riparian Ecosystem Restoration in Tropical Agriculture (RERTA) Project, which tests strategies for restoring riparian habitat; and (4) support for additional collaborative projects within the Programme landscape. Across all projects, we are measuring environmental conditions, biodiversity, and ecosystem functions. We also measure oil palm yield and production costs, in order to assess whether suggested sustainability strategies are feasible from an agronomic perspective. Early results show that oil palm plantation habitat is more variable than might be expected from a monoculture crop, and that everyday vegetation management decisions have significant impacts on habitat structure. The BEFTA Programme highlights the value of large-scale collaborative projects for understanding tropical agricultural systems, and offers a highly valuable experimental set-up for improving our understanding of practices to manage oil palm more sustainably. Published version This work was funded by The Isaac Newton Trust Cambridge, Golden Agri Resources, ICOPE (the International Conference on Oil Palm and the Environment), and the Natural Environment Research Council (grant number NE/P00458X/1). Open access publication was funded by the University of Cambridge’s Open Access Service, as a result of this project’s Research Council UK (RCUK) funding.

Marine management areas provide a key tool for efforts towards sustainable development, reconciling socio-economic goals with those for biodiversity conservation. Decisions about where and when to establish spatial management areas in the oceans are currently hampered by the uncertainties of incomplete, or overly general, information about biodiversity. The analysis of environmental DNA (eDNA) provides a potentially powerful tool to overcome this lack of data in the future. Here we present directions to develop robust approaches to integrate eDNA and spatial planning processes, aiming to provide guidance to underpin tool development. The potential of eDNA use in conservation is widely recognised, although direct applications almost exclusively focus on detection of invasive or threatened species and not spatial management decisions. The implementation of broader interaction between the fields of conservation science and eDNA analysis could create substantial benefits to biodiversity conservation and management. In particular, eDNA analysis can provide information on biodiversity over spatial-temporal scales that are currently prohibitive in spatial planning studies. Here, we provide an overview of how eDNA is currently used in conservation practice, in addition to understanding its limitations and benefits within the context of spatial planning. With the goal to harness rapid technological developments in both molecular and conservation sciences, we provide a horizon scan of the future of eDNA analysis and its application to inform biodiversity conservation in a rapidly changing world.

Summary There is consensus that plant species richness enhances plant productivity within natural grasslands, but the underlying drivers remain debated. Recently, differential accumulation of soil‐borne fungal pathogens across the plant diversity gradient has been proposed as a cause of this pattern. However, the below‐ground environment has generally been treated as a ‘black box’ in biodiversity experiments, leaving these fungi unidentified.Using next generation sequencing and pathogenicity assays, we analysed the community composition of root‐associated fungi from a biodiversity experiment to examine if evidence exists for host specificity and negative density dependence in the interplay between soil‐borne fungi, plant diversity and productivity.Plant species were colonised by distinct (pathogenic) fungal communities and isolated fungal species showed negative, species‐specific effects on plant growth. Moreover, 57% of the pathogenic fungal operational taxonomic units (OTUs) recorded in plant monocultures were not detected in eight plant species plots, suggesting a loss of pathogenic OTUs with plant diversity.Our work provides strong evidence for host specificity and negative density‐dependent effects of root‐associated fungi on plant species in grasslands. Our work substantiates the hypothesis that fungal root pathogens are an important driver of biodiversity‐ecosystem functioning relationships.

Tropical forests have long fascinated ecologists, inspiring a plethora of research into the mechanisms regulating their immense biodiversity, which originally captured the interests of early natural historians and explorers, and that still persists to this day. A new focus of this research emerged in the early 2000s highlighting the potential role of neutral (stochastic) processes in regulating the composition and diversity of tropical forest communities, and thus the maintenance of a large portion of global biodiversity (Hubbell, ). This strictly contrasted the long-held belief that communities assembled via the sorting of species (and their abundances) via a deterministic response to local abiotic and biotic environmental conditions, reflecting the niche of each species (Leibold & McPeek, ). Yet, it is unlikely that the assembly of any community is solely governed by either stochastic or deterministic processes, but instead a combination of both. However, whether deterministic processes via niche-based environmental sorting of species, or stochastic processes reflecting pattens of dispersal limitation, neutral effects and ecological drift dominate is often unclear. This prompts questions as to whether the relative influence of one process over another is dependent on the scale (spatial or temporal) or context of the study, or specific traits of the taxa under investigation (e.g., body size). In a From the Cover paper in this issue of Molecular Ecology, Zinger et al. () tackle all these issues and show, among other things, that for soil microbes and mesofauna from tropical forests, the relative contribution of stochastic and deterministic processes in assembling their communities is strongly dependent on the body size or the studied taxa.

Dissolved organic matter (DOM) concentration and quality were examined from Arctic lakes located in three clusters across south-west (SW) Greenland, covering the regional climatic gradient: cool, wet coastal zone; dry inland interior; and cool, dry ice-marginal areas. We hypothesized that differences in mean annual precipitation between sites would result in a reduced hydrological connectivity between lakes and their catchments and that this concentrates degraded DOM. The DOM in the inland lake group was characterized by a lower aromaticity and molecular weight, a low soil-like fluorescence, and carbon stable isotope (δ13C-DOC) values enriched by ~2‰ relative to the coastal group. DOC-specific absorbance (SUVA254) and DOC-specific soil-like fluorescence (SUVFC1) revealed seasonal and climatic gradients across which DOM exhibited a dynamic we term “pulse-process”: Pulses of DOM exported from soils to lakes during snow and ice melt were followed by pulses of autochthonous DOM inputs (possibly from macrophytes), and their subsequent photochemical and microbial processing. These effects regulated the dynamics of DOM in the inland lakes and suggested that if circumpolar lakes currently situated in cool wetter climatic regimes with strong hydrological connectivity have reduced connectivity under a drier future climate, they may evolve toward an end‐point of large stocks of highly degraded DOC, equivalent to the inland lakes in the present study. The regional climatic gradient across SW Greenland and its influence on DOM properties in these lakes provide a model of possible future changes to lake C cycling in high-latitude systems where climatic changes are most pronounced.

Here we investigate the effect of agricultural integrated management on soil microbial diversity within a vineyard with a history (20 years) of exposure to frequent applications of fertilizers and pesticides each season. Considering that these practices were mainly directed to the target plant (i.e. grapevine) and its surrounding area, we expected that these practices have influenced the soil alpha and beta bacterial and fungal diversity differently. Soil samples were collected from three different sites: row, inter-row (space between vines rows) and headland. The soil microbial community was investigated by targeted amplicon sequencing of the 16SrRNA gene (for bacteria) and the ITS region (for fungi), and the chemical and physical soil properties have been characterized. Soil samples collected in row and inter-row were chemically and microbiologically different from the headland soil (PERMANOVA: row/inter-row vs headland P ≤ 0.01), exhibiting this latter a significantly lower concentration of heavy metals. This soil heterogeneity seemed to play a crucial role in the variation of species diversity of microbial communities among sites (i.e. beta-diversity). In contrast, the mean species diversity in each site (i.e. alpha-diversity) did not change among the sites. The sole variation of the beta-diversity could indicate a possible turnover of soil microbial communities to agricultural practices without compromising the alpha-diversity values.

Broad-scale studies and regional comparisons of Indonesia’s coral reefs are critical given the relative lack of information about these large, diverse, and threatened ecosystems. Most studies on reef benthic composition and distribution have largely focused on rather short transects spanning relatively small areas. Here, we quantify the shallow large-scale spatial distribution of benthic communities in four locations in Eastern Indonesia, i.e. the Spermonde Archipelago in South Sulawesi, and Ambon, Halmahera and Lucipara in Maluku Islands. Shallow coral reef ecosystems (0.5-2 m depth) were assessed using a georeferenced photoquadrat survey method that can cover larger proportions of reefs, as well as benthic assemblages in deeper reefs ( ∼ 8 m depth) recorded with photoquadrats. A total of 27.8 km of shallow and 4.8 km of deeper reef ecosystem transects were surveyed in this study. We found that reef benthic communities at the study locations were mainly characterized by low to moderate cover of live hard corals and relatively high cover of dead corals or abiotic components. Ninety percent of the surveyed reefs at both depths exhibited 25% dead corals or abiotic components. A combination of georeferenced photoquadrats and CoralNet machine learning rapidly identified benthic composition across a large area, which is useful for mapping or other large-scale applications. This information can support decision-makers for better management of resources and marine spatial planning, crucial for an archipelagic state with tens of thousands of islands such as Indonesia. Our broad-scale reef surveying, focusing on under-studied areas of Indonesia, can contribute to this effort, as well as others seeking to better map coral reef habitats, as an important foundation for their conservation amidst growing threats.

International audience

Although desert soils support functionally important microbial communities that affect plant growth and influence many biogeochemical processes, the impact of future changes in precipitation patterns on the microbiota and their activities is largely unknown. We performed in-situ experiments to investigate the effect of simulated rainfall on bacterial communities associated with the widespread perennial shrub, Rhazya stricta in Arabian desert soils. The bacterial community composition was distinct between three different soil compartments: surface biological crust, root-attached, and the broader rhizosphere. Simulated rainfall had no significant effect on the overall bacterial community composition, but some population-level responses were observed, especially in soil crusts where Betaproteobacteria, Sphingobacteria, and Bacilli became more abundant. Bacterial biomass in the nutrient-rich crust increased three-fold one week after watering, whereas it did not change in the rhizosphere, despite its much higher water retention. These findings indicate that between rainfall events, desert-soil microbial communities enter into stasis, with limited species turnover, and reactivate rapidly and relatively uniformly when water becomes available. However, microbiota in the crust, which was relatively enriched in nutrients and organic matter, were primarily water-limited, compared with the rhizosphere microbiota that were co-limited by nutrients and water.

Anammox, an important N2 loss pathway in marine waters, is not well understood in rivers. In situ measurements of N2 production in UK rivers reveal that anammox can be the dominant N2 loss pathway in permeable but not in impermeable riverbeds. Rivers are an important global sink for excess bioavailable nitrogen: they convert approximately 40% of terrestrial N runoff per year (∼47 Tg) to biologically unavailable N2 gas and return it to the atmosphere1. At present, riverine N2 production is conceptualized and modelled as denitrification2,3,4. Anaerobic ammonium oxidation, known as anammox, is an alternative pathway of N2 production important in marine environments, but its contribution to riverine N2 production is not well understood5,6. Here we use in situ and laboratory measurements of anammox activity using 15N tracers and molecular analyses of microbial communities to evaluate anammox in clay-, sand- and chalk-dominated river beds in the Hampshire Avon catchment, UK during summer 2013. Abundance of the hzo gene, which encodes an enzyme central to anammox metabolism, varied across the contrasting geologies. Anammox rates were similar across geologies but contributed different proportions of N2 production because of variation in denitrification rates. In spite of requiring anoxic conditions, anammox, most likely coupled to partial nitrification, contributed up to 58% of in situ N2 production in oxic, permeable riverbeds. In contrast, denitrification dominated in low-permeability clay-bed rivers, where anammox contributes roughly 7% to the production of N2 gas. We conclude that anammox can represent an important nitrogen loss pathway in permeable river sediments.

The conditions that allow biodiversity to recover following severe environmental degradation are poorly understood. We studied community rescue, the recovery of a viable community through the evolutionary rescue of many populations within an evolving community, in metacommunities of soil microbes adapting to a herbicide. The metacommunities occupied a landscape of crossed spatial gradients of the herbicide (Dalapon) and a resource (glucose), whereas their constituent communities were either isolated or connected by dispersal. The spread of adapted communities across the landscape and the persistence of communities when that landscape was degraded were strongly promoted by dispersal, and the capacity to adapt to lethal stress was also related to community size and initial diversity. After abrupt and lethal stress, community rescue was most frequent in communities that had previously experienced sublethal levels of stress and had been connected by dispersal. Community rescue occurred through the evolutionary rescue of both initially common taxa, which remained common, and of initially rare taxa, which grew to dominate the evolved community. Community rescue may allow productivity and biodiversity to recover from severe environmental degradation.

The ecological impacts of long‐term elevated atmospheric CO2 (eCO2) levels on soil microbiota remain largely unknown. This is particularly true for the arbuscular mycorrhizal (AM) fungi, which form mutualistic associations with over two‐thirds of terrestrial plant species and are entirely dependent on their plant hosts for carbon. Here, we use high‐resolution amplicon sequencing (Illumina, HiSeq) to quantify the response of AM fungal communities to the longest running (>15 years) free‐air carbon dioxide enrichment (FACE) experiment in the Northern Hemisphere (GiFACE); providing the first evaluation of these responses from old‐growth (>100 years) semi‐natural grasslands subjected to a 20% increase in atmospheric CO2. eCO2 significantly increased AM fungal richness but had a less‐pronounced impact on the composition of their communities. However, while broader changes in community composition were not observed, more subtle responses of specific AM fungal taxa were with populations both increasing and decreasing in abundance in response to eCO2. Most population‐level responses to eCO2 were not consistent through time, with a significant interaction between sampling time and eCO2 treatment being observed. This suggests that the temporal dynamics of AM fungal populations may be disturbed by anthropogenic stressors. As AM fungi are functionally differentiated, with different taxa providing different benefits to host plants, changes in population densities in response to eCO2 may significantly impact terrestrial plant communities and their productivity. Thus, predictions regarding future terrestrial ecosystems must consider changes both aboveground and belowground, but avoid relying on broad‐scale community‐level responses of soil microbes observed on single occasions.

International audience; Air samples from four contrasting outdoor environments including a park, an arable farm, a waste water treatment plant and a composting facility were analysed during the summer and winter months. The aim of the research was to study the feasibility of differentiating microbial communities from urban, rural and industrial areas between seasons with chemical and molecular markers such as microbial volatile organic compounds (MVOCs) and phospholipid fatty acids (PLFAs). Air samples (3 l) were collected every 2 h for a total of 6 h in order to assess the temporal variations of MVOCs and PLFAs along the day. MVOCs and VOCs concentrations varied over the day, especially in the composting facility which was the site where more human activities were carried out. At this site, total VOC concentration varied between 80 and 170 μg m−3 in summer and 20–250 μg m−3 in winter. The composition of MVOCs varied between sites due to the different biological substrates including crops, waste water, green waste or grass. MVOCs composition also differed between seasons as in summer they are more likely to get modified by oxidation processes in the atmosphere and in winter by reduction processes. The composition of microbial communities identified by the analysis of PLFAs also varied among the different locations and between seasons. The location with higher concentrations of PLFAs in summer was the farm (7297 ng m−3) and in winter the park (11,724 ng m−3). A specific set of MVOCs and PLFAs that most represent each one of the locations was identified by principal component analyses (PCA) and canonical analyses. Further to this, concentrations of both total VOCs and PLFAs were at least three times higher in winter than in summer. The difference in concentrations between summer and winter suggest that seasonal variations should be considered when assessing the risk of exposure to these compounds.

Microorganisms are ubiquitous and represent a taxonomically and functionally diverse component of freshwater environments of significant ecological importance. The bacteria, archaea, and microbial eukarya in freshwater systems support a range of ecosystem processes and functions, including mediating all major biogeochemical cycles, and therefore regulate the flow of multiple ecosystem services. Yet relative to conspicuous higher taxa, microbial ecology remains poorly understood. As the anthropocene progresses, the demand for freshwater–ecosystem services is both increasing with growing human population density, and by association, increasingly threatened from multiple and often interacting stressors, such as climate change, eutrophication, and chemical pollution. Thus, it is imperative to understand the ecology of microorganisms and their functional role in freshwater ecosystems if we are to manage the future of these environments effectively. To do this, researchers have developed a vast array of molecular tools that can illuminate the diversity, composition, and activity of microbial communities. Within this primer, we discuss the history of molecular approaches in microbial ecology, and highlight the scope of questions that these methods enable researchers to address. Using some recent case studies, we describe some exemplar research into the microbial ecology of freshwater systems, and emphasize how molecular methods can provide novel ecological insights. Finally, we detail some promising developments within this research field, and how these might shape the future research landscape of freshwater microbial ecology.

Within soils there are microorganisms that act to break down complex substrates (saprophytes), microorganisms that actively aid nutrient delivery (mycorrhizal fungi and nitrogen-fixing bacteria), and others that hijack the system to their own benefit (parasitic bacteria and fungi). The complex interaction between plants, these microbes, and the soil determines how effectively nutrients will be recycled, with a significant impact on regional productivity and biodiversity. Each microbe plays a role in overall soil function but, despite the critical role they play, soil microbial communities and their functions remain challenging to accurately quantify. The functional behaviour of soils is difficult to quantify, in part due to the effects of disturbance when sampling. This suggests that noninvasive analytical tools are necessary to diagnose current soil function and to predict changes in soil behaviour with changing climate or land use. Microbial communities, the drivers of soil function, are diverse, and their individual metabolisms are often tightly coupled, such that the microbial community in aggregate may be considered to have a “net” metabolism. This net metabolism can be described by the volatile signatures that propagate from the soil into the atmosphere and, by proxy, allowing a noninvasive analysis of the microbial community active in the subsurface. Here, we detail the complexities of the soil volatile metabolism, propose a “fingerprint” strategy to describe this complex community that uses trace gas fluxes combined with environmental data, and describe the promising outcomes from an initial foray using this method.

All organisms and ecosystems emit and consume volatile organic compounds (VOCs). Traditionally, these have been qualitatively and quantitatively described in isolation without full consideration of the ‘signatures’ produced by the totality of all volatiles released. Here, we suggest that volatilomics, a research area applied to medical diagnostics, soil biology and pest control, can advance aquatic ecological research by providing a relatively fast diagnostic tool to investigate, for example, taxonomic and likely also functional diversity in aquatic systems—providing a novel technique for the biomonitoring of aquatic environments. Our case study demonstrates the utility of volatilomics to differentiate between four different algal genera using a principal component analysis. We highlight the utility of volatilomics to the monitoring of environmental processes and discuss its application to inform industrial mariculture procedures.

International audience; Ecological network analysis (ENA) provides a mechanistic framework for describing complex species interactions, quantifying ecosystem services, and examining the impacts of environmental change on ecosystems. In this chapter, we highlight the importance and potential of ENA in future biomonitoring programs, as current biomonitoring indicators (e.g. species richness, population abundances of targeted species) are mostly descriptive and unable to characterize the mechanisms that underpin ecosystem functioning. Measuring the robustness of multilayer networks in the long term is one way of integrating ecological metrics more generally into biomonitoring schemes to better measure biodiversity and ecosystem functioning. Ecological networks are nevertheless difficult and labour-intensive to construct using conventional approaches, especially when building multilayer networks in poorly studied ecosystems (i.e. many tropical regions). Next-generation sequencing (NGS) provides unprecedented opportunities to rapidly build highly resolved species interaction networks across multiple trophic levels, but are yet to be fully exploited. We highlight the impediments to ecologists wishing to build DNA-based ecological networks and discuss some possible solutions. Machine learning and better data sharing between ecologists represent very important areas for advances in NGS-based networks. The future of network ecology is very exciting as all the tools necessary to build highly resolved multilayer networks are now within ecologists reach.

Coral communities are increasingly found to populate non-reef habitats prone to high environmental variability. Such sites include seagrass meadows, which are generally not considered optimal habitats for corals as a result of limited suitable substrate for settlement and substantial diel and seasonal fluctuations in physicochemical conditions relative to neighboring reefs. Interest in understanding the ability of corals to persist in non-reef habitats has grown, however little baseline data exists on community structure and recruitment of scleractinian corals in seagrass meadows. To determine how corals populate seagrass meadows, we surveyed the established and recruited coral community over 25 months within seagrass meadows at Little Cayman, Cayman Islands. Simultaneous surveys of established and recruited coral communities at neighboring back-reef sites were conducted for comparison. To fully understand the amount of environmental variability to which corals in each habitat were exposed, we conducted complementary surveys of physicochemical conditions in both seagrass meadows and back-reefs. Despite overall higher variability in physicochemical conditions, particularly pH, compared to the back-reef, 14 coral taxa were capable of inhabiting seagrass meadows, and multiple coral families were also found to recruit to these sites. However, coral cover and species diversity, richness, and evenness were lower at sites within seagrass meadows compared to back-reef sites. Although questions remain regarding the processes governing recruitment, these results provide evidence that seagrass beds can serve as functional habitats for corals despite high levels of environmental variability and suboptimal conditions compared to neighboring reefs.

Deciphering the ecology of marine obligate hydrocarbonoclastic bacteria (MOHCB) is of crucial importance for understanding their success in occupying distinct niches in hydrocarbon-contaminated marine environments after oil spills. In marine coastal sediments, MOHCB are particularly subjected to extreme fluctuating conditions due to redox oscillations several times a day as a result of mechanical (tide, waves and currents) and biological (bioturbation) reworking of the sediment. The adaptation of MOHCB to the redox oscillations was investigated by an experimental ecology approach, subjecting a hydrocarbon-degrading microbial community to contrasting oxygenation regimes including permanent anoxic conditions, anoxic/oxic oscillations and permanent oxic conditions. The most ubiquitous MOHCB, Alcanivorax and Cycloclasticus, showed different behaviors, especially under anoxic/oxic oscillation conditions, which were more favorable for Alcanivorax than for Cycloclasticus. The micro-diversity of 16S rRNA gene transcripts from these genera revealed specific ecotypes for different oxygenation conditions and their dynamics. It is likely that such ecotypes allow the colonization of distinct ecological niches that may explain the success of Alcanivorax and Cycloclasticus in hydrocarbon-contaminated coastal sediments during oil-spills.