Communities Of Organisms Research Articles

Lithology and disturbance drive cavefish and cave crayfish occurrence in the Ozark Highlands ecoregion

Diverse communities of groundwater-dwelling organisms (i.e., stygobionts) are important for human wellbeing; however, we lack an understanding of the factors driving their distributions, making it difficult to protect many at-risk species. Therefore, our study objective was to determine the landscape factors related to the occurrence of cavefishes and cave crayfishes in the Ozark Highlands ecoregion, USA. We sampled cavefishes and cave crayfishes at 61 sampling units using both visual and environmental DNA surveys. We then modeled occurrence probability in relation to lithology and human disturbance while accounting for imperfect detection. Our results indicated that occurrence probability of cave crayfishes was negatively associated with human disturbance, whereas there was a weak positive relationship between cavefish occurrence and disturbance. Both cavefishes and cave crayfishes were more likely to occur in limestone rather than dolostone lithology. Our results indicate structuring factors are related to the distribution of these taxa, but with human disturbance as a prevalent modifier of distributions for cave crayfishes. Limiting human alteration near karst features may be warranted to promote the persistence of some stygobionts. Moreover, our results indicate current sampling efforts are inadequate to detect cryptic species; therefore, expanding sampling may be needed to develop effective conservation actions.

Metabarcoding for biodiversity inventory blind spots: A test case using the beetle fauna of an insular cloud forest.

Soils harbour a rich arthropod fauna, but many species are still not formally described (Linnaean shortfall) and the distribution of those already described is poorly understood (Wallacean shortfall). Metabarcoding holds much promise to fill this gap, however, nuclear copies of mitochondrial genes, and other artefacts lead to taxonomic inflation, which compromise the reliability of biodiversity inventories. Here, we explore the potential of a bioinformatic approach to jointly "denoise" and filter nonauthentic mitochondrial sequences from metabarcode reads to obtain reliable soil beetle inventories and address open questions in soil biodiversity research, such as the scale of dispersal constraints in different soil layers. We sampled cloud forest arthropod communities from 49 sites in the Anaga peninsula of Tenerife (Canary Islands). We performed whole organism community DNA (wocDNA) metabarcoding, and built a local reference database with COI barcode sequences of 310 species of Coleoptera for filtering reads and the identification of metabarcoded species. This resulted in reliable haplotype data after considerably reducing nuclear mitochondrial copies and other artefacts. Comparing our results with previous beetle inventories, we found: (i) new species records, potentially representing undescribed species; (ii) new distribution records, and (iii) validated phylogeographic structure when compared with traditional sequencing approaches. Analyses also revealed evidence for higher dispersal constraint within deeper soil beetle communities, compared to those closer to the surface. The combined power of barcoding and metabarcoding contribute to mitigate the important shortfalls associated with soil arthropod diversity data, and thus address unresolved questions for this vast biodiversity fraction.

Best Practices to Promote Data Utility and Reuse by the Non-Traditional Model Organism Community.

The dramatic increase in accessibility to sequencing technologies has opened new avenues into studying different processes, cells, and animal models. In the amphibian models used for regeneration research, these new datasets have uncovered a variety of information about what genes define the regenerating limb as well as how genes and cells change over the course of regeneration. The accumulation of data from these studies undoubtedly increases our understanding of regeneration. Throughout these studies, it is important to consider how data can be made most useful not only for the primary study but also for reuse within the scientific community. This chapter will focus on best practices for data collection and handling as well as principles to promote access and reuse of big datasets. However, the deposition and thorough description of data of all sizes generated for a publication (e.g., images, fcs files, etc.) can also be done following this generic workflow. The aim is to lower hurdles for reuse, access, and re-evaluation of data which will in turn increase the utility of these datasets and accelerate scientific progress.

Benchmarking Community-Wide Estimates of Growth Potential from Metagenomes Using Codon Usage Statistics.

ABSTRACTTrait inference from mixed-species assemblages is a central problem in microbial ecology. Frequently, sequencing information from an environment is available, but phenotypic measurements from individual community members are not. With the increasing availability of molecular data for microbial communities, bioinformatic approaches that map metagenome to (meta)phenotype are needed. Recently, we developed a tool, gRodon, that enables the prediction of the maximum growth rate of an organism from genomic data on the basis of codon usage patterns. Our work and that of other groups suggest that such predictors can be applied to mixed-species communities in order to derive estimates of the average community-wide maximum growth rate. Here, we present an improved maximum growth rate predictor designed for metagenomes that corrects a persistent GC bias in the original gRodon model for metagenomic prediction. We benchmark this predictor with simulated metagenomic data sets to show that it has superior performance on mixed-species communities relative to earlier models. We go on to provide guidance on data preprocessing and show that calling genes from assembled contigs rather than directly from reads dramatically improves performance. Finally, we apply our predictor to large-scale metagenomic data sets from marine and human microbiomes to illustrate how community-wide growth prediction can be a powerful approach for hypothesis generation. Altogether, we provide an updated tool with clear guidelines for users about the uses and pitfalls of metagenomic prediction of the average community-wide maximal growth rate.IMPORTANCE Microbes dominate nearly every known habitat, and therefore tools to survey the structure and function of natural microbial communities are much needed. Metagenomics, in which the DNA content of an entire community of organisms is sequenced all at once, allows us to probe the genetic diversity contained in a habitat. Yet, mapping metagenomic information to the actual traits of community members is a difficult and largely unsolved problem. Here, we present and validate a tool that allows users to predict the average maximum growth rate of a microbial community directly from metagenomic data. Maximum growth rate is a fundamental characteristic of microbial species that can give us a great deal of insight into their ecological role, and by applying our community-level predictor to large-scale metagenomic data sets from marine and human-associated microbiomes, we show how community-wide growth prediction can be a powerful approach for hypothesis generation.

Species as conservation umbrellas: A case study with lesser prairie-chicken (Tympanuchus pallidicinctus) in the southern Great Plains of North America

Conservation efforts often focus on a single species, but this approach is inefficient for agencies dealing with many declining species at risk of extinction. Leveraging already-funded management for additional species can help stretch limited resources to conserve more biodiversity. However, evaluation of the efficacy of such an umbrella approach is typically lacking, does not explicitly consider outcomes of management treatments, or only evaluates one or a few species. We developed a method to evaluate the ability of management for the lesser prairie-chicken (Tympanuchus pallidicinctus) to offer an umbrella of protection for non-target species at risk of decline. To accomplish this, we predicted the conservation outcomes of lesser prairie-chicken management for overlapping at-risk species and created an index of conservation benefit to evaluate the effectiveness of the lesser prairie-chicken as an umbrella species for conservation. We conducted a literature review for 77 at-risk species that overlap in range with the lesser prairie-chicken to determine the effects (benefit, cost, or neutral) of the primary conservation actions taken to manage lesser prairie-chicken habitat. We determined that 84 % of the species were expected to receive a net conservation benefit from management for lesser prairie-chicken, 8 % would incur a net cost, and 8 % would have a net balance of costs and benefits. These results suggest that the lesser prairie-chicken functions as an umbrella of protection for other grassland species, providing a net conservation benefit. Our index-based approach serves as a model for evaluating the efficacy of proposed surrogate species on a community of organisms.

Body size as key trait determining aquatic metacommunity assemblies in benthonic and planktonic habitats of Dongting Lake, China

• Aquatic community diversity decreased with increasing body size. • Body size affected distance-decay relationship of benthonic communities. • Higher effects of body size on benthonic community assembly than planktonic one. • Biotic interactions between microbial species were mediated by their body sizes. Body size play a key role in driving bioecological patterns by affecting community assembly processes at the organism level. However, the extent to which the relative influences of ecological processes operating community assembly with different body sizes at different habitat types in freshwater ecosystem is still unclear. Here, we conducted a comprehensive biodiversity survey on bacterial, fungal and invertebrate communities in planktonic and benthonic habitats of Dongting Lake, China, and evaluated the biogeographic distribution pattern and community assembly processes of distinct organism groups with different body sizes. Significant negative relationships between body size and community diversity indexes were observed in two habitats, and significant relationship between body size and distance-decay relationship was only observed in benthonic habitat. Body size showed stronger correlations with the ecological processes and ecological interactions of distinct organisms in benthonic habitat. Specifically, body size showed significantly positive correlation with the relative influence of deterministic processes which controlled the microbial community assembly processes, whereas body size was significantly positively correlated with stochastic processes in zoobenthos community. Molecular ecological network analyses also found that the average clustering coefficients and among-module connectivity were significantly negatively and positively correlated with their corresponding body size, respectively. Slops of correlations between body size and these parameters (including the null deviation value, dispersal rate, niche breadth and among-module connectivity) were steeper in benthonic habitat than that in planktonic habitat. Our findings suggested that body size operated the aquatic organism community assembly to affect their biogeographic distribution pattern, and the effect was stronger in benthonic habitat than in planktonic habitat. This study provides a better understanding of the mechanisms supporting the aquatic biodiversity on the sight of organism life-history trait.

Biological influences on coastal muddy sediment structure following resuspension

AbstractShallow coastal muddy sediments are important for global nutrient cycling and carbon storage and provide a habitat for diverse communities of organisms. Bottom shear stress from physical disturbances such as storms and hurricanes resuspend coastal muds, disrupting their cohesive structure. How biological vs. physical processes affect reconsolidation of physically disturbed natural muds, however, is poorly understood. We compare the recovery of sediment properties related to compaction and cohesion of muds following physical disturbance. We hypothesized that recovery of cohesion would take longer than compaction and that changes in surface and subsurface cohesion would occur on different timescales. We collected muddy sediment cores and resuspended the top 5 cm in the lab to simulate storm disturbance. At several timepoints following resuspension (1–30 d), we measured sediment properties providing metrics of compaction (sediment height, porosity, grain size distribution, sound speed) and of surface and subsurface cohesion (erodibility, fracture behavior, exopolymeric substances [EPS]). Compaction and cohesion increased rapidly over the first 1–2 d after resuspension and continued to slowly increase for 2 weeks. Between 2 and 4 weeks, however, subsurface cohesion increased and turbidity decreased, consistent with sediment restabilization. In contrast, subsurface compaction decreased and eroded mass increased, suggesting destabilization. We attribute this apparent destabilization to delayed activity of small‐bodied infauna. Surprisingly, EPS concentration did not explain cohesion changes. These results highlight the importance of including biological parameters when predicting the recovery of sediment structure following a physical disturbance. This work has implications for understanding coastal sediment transport dynamics in frequently disturbed sediments.

Distribution characteristics of terrestrial and marine lipid biomarkers in surface sediment and their implication for the provenance and palaeoceanographic application in the northern South China Sea

Multi biolipids, including plant wax, algal biomarkers, and glycerol dialkyl glycerol tetraethers (GDGTs), were studied in surface sediments of the northern South China Sea (SCS). Unusual elevated contents of odd n-alkanes (C27, C29, C31) and even n-alkanols (C22, C24, C26) derived from terrestrial plant wax in the outer shelf areas indicated the strong influence of deep-water counter current in redistributing and deposition of Taiwan Island sourced organic matter (OM) in the northern SCS. The spatial distribution of dinosterol and brassicasterol (corresponding to dinoflagellates and diatoms of high competitive advantage for nutrients), respectively, displayed a high abundance near the Pearl River Estuary (PRE), southwest off Taiwan Island, and southeast off Hainan Island, in contrast to the relatively high biomass of C37-alkenones, C30-diol/ketol and isoprenoid GDGTs (iGDGTs) in the outer shelf oligotrophic areas, indicating their feasibility in marine productivity reconstruction. The observed high contents of alkenones than brassicasterol in the sediment, albeit the overall dominance of diatoms in the SCS surface water, showed differences in the degradation and/or preservation efficiency of different organic lipids in sediments. The influences of season, source organisms, and different regression methods on the sea surface temperatures (SST) reconstruction were also evaluated in the region extending from shelf to deep water. The reconstructed SSTs based on U37K' mainly reflected spring SSTs, indicating the influence of growing seasons on the source organism. The reconstructed TEX86 SST corresponded more with the mean annual SST in the northern SCS, mainly in the deep-water regions. Changes in the total composition of the archaeal community and population is suggested to be the major factor causing the unusually low and wide range of TEX86 SSTs in the nearshore areas. The combination of the two organic paleothermometers offers complementary information on SST developments in the northern SCS. Multi-biomarkers study in the present work indicates the feasibility of lipids in paleoecology and paleoclimate reconstruction. However, care must be taken in palaeoceanographic reconstruction due to complex hydrological and biological influence, i.e., the deep lateral current on the continental matter transportation, the differential degradation of various organic lipids, and the different seasonal and/or source organism community bias on the organic thermometer in the study area.

Monitoring of heavy metals and essential trace elements in aquatic plant Ranunculus sphaerospermus Boiss. & Blanche (Ranunculaceae), sediments, and water of volcanic Haydarlar Lake, Türkiye

Aquatic ecosystems contain communities of organisms that are dependent on each other and on their environment. Monitoring of trace element and heavy metal concentrations is important to understand the possible environmental risks in natural aquatic environments. In the present study, concentrations of some heavy metals and trace elements in aquatic plant Ranunculus sphaerospermus, sediments, and water samples of volcanic Haydarlar Lake were analyzed by using ICP-OES. The concentrations were found in the following ranges: 82.11 – 97.38, 9174.50 – 9942.29, and 0.63 – 0.89 for Al; 10.29 – 17.43, 30.60 – 55.60, and 0.81 – 0.98 for B; 1038.44 – 1682.30, 4017.26 – 4503.54, and 1276.61 – 1541.41 for Ca; 120.69 – 178.41, 6894.50 – 8103.47, and 0.51 – 0.69 for Fe; 2503.51 – 2983.38, 1118.50 – 1693.38, and 69.43 – 93.82 for K; 563.38 – 783.22, 885.32 – 1122.47, and 108.55 – 143.36 for Mg in the plant (mg kg−1), sediment (mg kg−1), and water (mg L−1) samples, respectively. The concentrations of Ca, Fe, and K elements in sediments and the content of Ca and K in lake water samples were found as higher than the acceptable limit, while concentrations of all elements in R. sphaerospermus were determined to be within acceptable limits. Transfer factors (TF) of the heavy metal and essential elements from sediment to the plant samples were evaluated. The trends of TF for all samples studied were in the following order; K>Mg>B>Ca>Fe>Al. Consequently, the approach used in this study could contribute to pollution monitoring in the future.

Sympatric soil biota mitigate a warmer-drier climate for Bouteloua gracilis.

Climate change is altering temperature and precipitation, resulting in widespread plant mortality and shifts in plant distributions. Plants growing in soil types with low water holding capacity may experience intensified effects of reduced water availability as a result of climate change. Furthermore, complex biotic interactions between plants and soil organisms may mitigate or exacerbate the effects of climate change. This 3-year field experiment observed the performance of Bouteloua gracilis ecotypes that were transplanted across an environmental gradient with either sympatric soil from the seed source location or allopatric soil from the location that plants were transplanted into. We also inoculated plants with either sympatric or allopatric soil biotic communities to test: (1) how changes in climate alone influence plant growth, (2) how soil types interact with climate to influence plant growth, and (3) the role of soil biota in mitigating plant migration to novel environments. As expected, plants moved to cooler-wetter sites exhibited enhanced growth; however, plants moved to warmer-drier sites responded variably depending on the provenance of their soil and inoculum. Soil and inoculum provenance had little influence on the performance of plants moved to cooler-wetter sites, but at warmer-drier sites they were important predictors of plant biomass, seed set, and specific leaf area. Specifically, transplants inoculated with their sympatric soil biota and grown in their sympatric soil were as large as or larger than reference plants grown at the seed source locations; however, individuals inoculated with allopatric soil biota were smaller than reference site individuals at warmer, drier sites. These findings demonstrate complicated plant responses to various aspects of environmental novelty where communities of soil organisms may help ameliorate stress. The belowground microbiome of plants should be considered to predict the responses of vegetation more accurately to climate change.

Intra-habitat structural complexity drives the distribution of fish trait groups on coral reefs

Three-dimensional (3D) habitat complexity is a primary driver of organism distribution and community structure across ecosystems. Identifying the specific metrics and spatial scales at which complexity is functionally important for communities is therefore a critical component in forecasting ecosystem function. Here we pair fish species traits with multiple metrics from habitat photogrammetry to evaluate the most important measures and scales of 3D complexity driving ecological functions within one of the most structurally diverse ecosystems on the planet: coral reefs. From May to July 2019, we collected high-resolution (1 cm) large- and small-scale intra-habitat (25 m2) structural complexity data across eight reefscapes (∼2500 m2) and conducted co-located fish functional group surveys in the Florida Keys, FL, USA. We used a hierarchical clustering analysis to group 80 observed fish species by four traits related to habitat use (social level, body size, crypsis, activity period) and feeding guild to generate mechanistic predictions about fish-habitat relationships. Evaluating relationships between the resulting trait-based functional groups (k = 9) and four metrics of intra-habitat complexity (large-scale vertical relief, and small-scale vector ruggedness [VRM], VRM deviation, and profile curvature) revealed that trait groups respond independently to the various measures and scales of reef complexity. While large-scale complexity (relief) is strongly related to the presence of solitary, cryptic, nocturnal carnivores, likely due to prey availability as well as day-time refuge opportunities, herbivore abundance is unaffected by increasing vertical relief, potentially due to predator avoidance. Instead, gregarious (i.e., schooling) herbivores increase with small-scale complexity measured by VRM and VRM deviation across reefscapes, while less gregarious herbivores only respond to small-scale complexity when these same measures occur in low-relief habitat, possibly due to a tradeoff between grazing resource availability and predator visibility. Our results reveal how unique elements of complexity provided by both biotic benthic communities as well as large-scale habitat features like vertical relief are differentially important to fish functional groups. The general relationships we identified using traits provide a framework for predicting fish community responses to changes in specific measures of structural complexity on coral reefs globally. Our work illustrates how preserving 3D habitat complexity by protecting or augmenting (e.g., via restoration) structure-forming organisms can support diverse organismal communities and overall ecosystem productivity.

COMMUNITY STRUCTURE OF GASTROPODS IN THE COASTAL WATERS OF NORTH RUPAT DISTRICT

Community structure is a concept that studies the composition or composition of species and abundance in a community. Coastal waters are areas with a depth of less than 200 meters and there is a littoral area located between the highest tide and the lowest low tide or called the intertidal area. One of the community of organisms in this intertidal area is gastropods. This research was conducted from December 2021 to January 2022. The purpose of the study was to determine the structure of the gastropod community in the coastal waters of North Rupat District consisting of species, density, diversity index, uniformity index, dominance index, distribution pattern, and community similarity. As supporting data in this study, several environmental parameters were also measured which included water quality, sediment type and sediment organic matter content. The research method used is a survey method, where sampling using the quadrant transect method is carried out at 3 stations. Based on the results of the study found 14 species of gastropods. The species that were found in all stations were Indothais gradata. Gastropod density is 15.800 ind/ha. Diversity index value (H') 1.85, uniformity index (E) 0.70, dominance index (C) 0.24, distribution pattern (Id) 3.24 is clustered, species similarity index (Ss) between stations Tanjung Medang and Teluk Rhu 83% of species are almost the same and between stations Tanjung Medang and Tanjung Punak 15% and between stations Teluk Rhu and Tanjung Punak 17% are not the same. Water quality parameters as follows: temperature 27-28oC; salinity 30-31 ppt; pH 6-7. Sediment organic matter 0.50-2.28%, sand sediment type

Illuminating protist diversity in pitcher plants and bromeliad tanks.

Many species of plants have evolved structures called phytotelmata that store water and trap detritus and prey. These structures house diverse communities of organisms, the inquiline microbiome, that aids breakdown of litter and prey. The invertebrate and bacterial food webs in these systems are well characterized, but less is known about microbial eukaryotic community dynamics. In this study we focus on microbes in the SAR clade (Stramenopila, Alveolata, Rhizaria) inhabiting phytotelmata. Using small subunit rDNA amplicon sequencing from repeated temporal and geographic samples of wild and cultivated plants across the Northeast U.S.A., we demonstrate that communities are variable within and between host plant type. Across habitats, communities from tropical bromeliads grown in a single room of a greenhouse were nearly as heterogeneous as wild pitcher plants spread across hundreds of kilometers. At the scale of pitcher plants in a single bog, analyses of samples from three time points suggest that seasonality is a major driver of protist community structure, with variable spring communities transitioning to more homogeneous communities that resemble the surrounding habitat. Our results indicate that protist communities in phytotelmata are variable, likely due to stochastic founder events and colonization/competition dynamics, leading to tremendous heterogeneity in inquiline microeukaryotic communities.

Trust your gut: The human microbiome

All mucosal surfaces of the human body are home to vast, complex communities of microbial organisms. These multitudes of non-pathological microbes are otherwise known as the human ‘microbiome’. It is only in recent years with developments in genome coding, that we are beginning to comprehend the significance of the microbiome on host physiology and disease. These microbes, once considered malevolent, have now become high profile in the media. The phrases ‘gut health’ and ‘microbiome’ are referred to across a range of industries and social media. This surge in interest may signal the potential for exciting developments and novel therapies. However, with such burgeoning public interest come new areas of debate, misinformation, and unanswered questions. This article provides an overview of: what the microbiome is, its function, its impact on disease and areas of ongoing research. This may enable clinicians to give evidence-based information to patients presenting with questions in practice.

562 Tinea pedis: Evidence for a dysbiosis of the foot microbiome

Historically, Trichophyton rubrum has been identified as the causative agent of the disease, Tinea pedis. Treatment options focus on the use of antifungals; however, antifungals have modest efficiency for clearing T. rubrum with high rates of reinfection and disease reoccurrence. Here we propose that T. pedis is not a simple fungal infection but a complex dysbiosis characterized by changes of the fungal and bacterial profile of the microbiome, with Trichophyton being an indicator of the disease. In this study, we used metagenomic sequencing to compare the microbiome composition of the interdigital toe web-space, nail bed, and plantar aspect in a population of individuals with T. pedis simple (n=26), T. pedis complex (n=25), and T. pedis moccasin (n=25) against 33 healthy volunteers and their matching anatomical sites. Metagenomic sequencing demonstrated differences in beta diversity and key species distinctions between diseased (T. pedis) and healthy states. We found that beta diversity differs greatly between these two groups, and that the microbiomes of individuals with T. pedis were significantly more similar to each other than the micobiomes of healthy individuals. There are also robust marker species denoting both T. pedis and healthy states. Specifically, Trichophyton was found in both healthy and diseased subjects but higher in abundance for T. pedis subjects. Other fungi had similar co-associations with the disease state. Bacterial co-occurrences with Corynebacterium resistens had the highest association in subjects with T. pedis, while Staphylococcus hominis and S. epidermidis were significantly higher in healthy individuals as compared to individuals with T. pedis. These results indicate that T. pedis is not a strict infection model of disease, but rather a dysbiosis associated with a community of organisms. A therapeutic approach to repair the dysbiosis has the potential for a more effective diagnostic and treatment plan for patients, with better long-term outcomes.

Relative species abundance and population densities of the past: developing multispecies occupancy models for fossil data

AbstractThe number of individuals of species varies, but estimating abundance, given incomplete and biased sampling in both contemporary and fossilized communities, is challenging. Here, we describe a new occupancy model in a hierarchical Bayesian framework with random effects, in which multispecies occupancy and detection are modeled as a means to estimate relative species abundance and relative population densities. The modeling framework is suited for temporal samples of fossil communities with repeated sampling including multiple species with similar preservation potential. We demonstrate our modeling framework using a fossil community of benthic organisms to estimate relative species abundance dynamics and changing relative population densities of focal species in nine (geological) time intervals over 2.3 Myr. We also explore potential explanatory factors (paleoenvironmental proxies) and temporal autocorrelation that could provide extra information on unsampled time intervals. The modeling framework is applicable across a wide range of questions on species-level dynamics in paleoecological community settings.

Detection of biofilm and planktonic microbial communities in litter/soil mixtures

Microbial community of the soil can be subdivided into a planktonic community of motile organisms and a community of sessile organisms, including those constituting biofilms on physical surfaces of different texture. Biofilm communities on surfaces of organic particles represent a crucial factor involved in decomposition of plant litter and soil particulate organic matter in general. In spite of their great ecological importance, the composition of soil biofilm communities is only scarcely studied due to methodological problems connected with distinguishing biofilm inhabitants from other soil organisms.In this study, we were able to distinguish microbial communities colonizing four compartments of the experimental system: particles of the litter/soil mixture, biofilms on adjacent smooth or fibrous glass surfaces, and plankton. Existence of different preferences of microbial operational taxonomic units (OTUs) to occupy the experimental compartments has been suggested on the basis of their relative abundance in the community. Three main OTU groups have been defined according to these preferences. They are tentatively termed generalists, OTUs corresponding to organisms preferring the litter particles and OTUs corresponding to selective organisms discriminating between different surface types. At the same time, temperature has been identified as a factor influencing the switching between preferences of organisms for experimental compartments. Our work contributes to the description of the spatial microscale distribution of microorganisms in soil containing decomposing organic matter.

Nasal microbiota evolution within the congregate setting imposed by military training

The human microbiome is comprised of a complex and diverse community of organisms that is subject to dynamic changes over time. As such, cross-sectional studies of the microbiome provide a multitude of information for a specific body site at a particular time, but they fail to account for temporal changes in microbial constituents resulting from various factors. To address this shortcoming, longitudinal research studies of the human microbiome investigate the influence of various factors on the microbiome of individuals within a group or community setting. These studies are vital to address the effects of host and/or environmental factors on microbiome composition as well as the potential contribution of microbiome members during the course of an infection. The relationship between microbial constituents and disease development has been previously explored for skin and soft tissue infections (SSTIs) within congregate military trainees. Accordingly, approximately 25% of the population carries Staphylococcus aureus within their nasal cavity, and these colonized individuals are known to be at increased risk for SSTIs. To examine the evolution of the nasal microbiota of U.S. Army Infantry trainees, individuals were sampled longitudinally from their arrival at Fort Benning, Georgia, until completion of their training 90 days later. These samples were then processed to determine S. aureus colonization status and to profile the nasal microbiota using 16S rRNA gene-based methods. Microbiota stability differed dramatically among the individual trainees; some subjects exhibited great stability, some subjects showed gradual temporal changes and some subjects displayed a dramatic shift in nasal microbiota composition. Further analysis utilizing the available trainee metadata suggests that the major drivers of nasal microbiota stability may be S. aureus colonization status and geographic origin of the trainees. Nasal microbiota evolution within the congregate setting imposed by military training is a complex process that appears to be affected by numerous factors. This finding may indicate that future campaigns to prevent S. aureus colonization and future SSTIs among high-risk military trainees may require a ‘personalized’ approach.

RepBin: Constraint-Based Graph Representation Learning for Metagenomic Binning

Mixed communities of organisms are found in many environments -- from the human gut to marine ecosystems -- and can have profound impact on human health and the environment. Metagenomics studies the genomic material of such communities through high-throughput sequencing that yields DNA subsequences for subsequent analysis. A fundamental problem in the standard workflow, called binning, is to discover clusters, of genomic subsequences, associated with the constituent organisms. Inherent noise in the subsequences, various biological constraints that need to be imposed on them and the skewed cluster size distribution exacerbate the difficulty of this unsupervised learning problem. In this paper, we present a new formulation using a graph where the nodes are subsequences and edges represent homophily information. In addition, we model biological constraints providing heterophilous signal about nodes that cannot be clustered together. We solve the binning problem by developing new algorithms for (i) graph representation learning that preserves both homophily relations and heterophily constraints (ii) constraint-based graph clustering method that addresses the problems of skewed cluster size distribution. Extensive experiments, on real and synthetic datasets, demonstrate that our approach, called RepBin, outperforms a wide variety of competing methods. Our constraint-based graph representation learning and clustering methods, that may be useful in other domains as well, advance the state-of-the-art in both metagenomics binning and graph representation learning.

Community assembly and metaphylogeography of soil biodiversity: Insights from haplotype-level community DNA metabarcoding within an oceanic island.

Most of our understanding of island diversity comes from the study of aboveground systems, while the patterns and processes of diversification and community assembly for belowground biotas remain poorly understood. Here, we take advantage of a relatively young and dynamic oceanic island to advance our understanding of ecoevolutionary processes driving community assembly within soil mesofauna. Using whole organism community DNA (wocDNA) metabarcoding and the recently developed metaMATE pipeline, we have generated spatially explicit and reliable haplotype‐level DNA sequence data for soil mesofaunal assemblages sampled across the four main habitats within the island of Tenerife. Community ecological and metaphylogeographic analyses have been performed at multiple levels of genetic similarity, from haplotypes to species and supraspecific groupings. Broadly consistent patterns of local‐scale species richness across different insular habitats have been found, whereas local insular richness is lower than in continental settings. Our results reveal an important role for niche conservatism as a driver of insular community assembly of soil mesofauna, with only limited evidence for habitat shifts promoting diversification. Furthermore, support is found for a fundamental role of habitat in the assembly of soil mesofauna, where habitat specialism is mainly due to colonization and the establishment of preadapted species. Hierarchical patterns of distance decay at the community level and metaphylogeographical analyses support a pattern of geographic structuring over limited spatial scales, from the level of haplotypes through to species and lineages, as expected for taxa with strong dispersal limitations. Our results demonstrate the potential for wocDNA metabarcoding to advance our understanding of biodiversity.