Community Dissimilarity Research Articles

Characterization of marine eukaryotic biofilms at offshore wind farm sites: assessment of DNA extraction methods and marker gene used for metabarcoding approaches

Among marine lifestyles, biofilms are considered as diversified communities embedded in complex exopolymers whose development depends on several factors, related to both environmental conditions and physical-chemical characteristics of substrates (Antunes et al. 2019, Bellou et al. 2012). For the maritime industry, bio-colonization and its impact on human activities were well-described (Schultz et al. 2011). However, this phenomenon represents a new challenge in Renewable Marine Energies (RME) due to their specificities (materials, structures, localization…). In particular, macro-organism assemblages appeared to include a wide variety of eukaryotic groups but the literature is sparse considering the sequencing of eukaryotic diversity in comparison to those of bacterial communities (Briand et al. 2018, Dang and Lovell 2000, Salta et al. 2013). As a matter of fact, the very small size of some of the eukaryotes and/or their insufficient morphological discernible features appear to considerably limit their detection and identification, leading to underestimate their diversity (Carugati et al. 2015). When talking about molecular approaches, analysis of eukaryotes also represents a challenge because such organisms possess resilient cellular structures which can give poor DNA extraction yield (Hermans et al., 2018Hermans et al. 2018). In addition, SSU rRNA in eukaryotes fails to be as universal as for prokaryotes (Bik et al. 2012, Medinger et al. 2010). However, the use of marker genes from environmental DNA, when focused on the targeted eukaryotic community, remains critical to decoding the complexity of marine biofilms diversity. In this study, four extraction methods, including a preliminary mechanic cell lysis, both soil and biofilm kits, and global approaches, have been compared. We also examined the coverage and the identification capability of several primers to characterize eukaryotic communities colonizing three plastic surface types (polyvinyl chloride, HD polyethylene, and polyamide) which have been immersed in several locations along the French Mediterranean and Atlantic coasts. Sequence quality and number remain the same whatever the extraction method. However, the richness and community structure were clearly affected regardless of the sample type (Figure 1). Finally, two kits (PowerMaxSoil, and PowerBiofilm kits) evaluated in this study were considered as the most powerful overall. Secondly, we amplified and sequenced short fragments of two genes: one region of the mitochondrial Cytochrome Oxidase subunit I (COI) and five variable regions of the 18S small subunit ribosomal DNA (rDNA) gene (V1V2, V4TAR, V4UNI, V7, and V9). The Chao1 index was considerably lower for the CO1 gene compared to those of the 18S rDNA regions. The V4TAR and V7 regions showed a significant highest richness, followed closely by the V1V2 and V9 regions. The 18S rDNA gene sequences were dominated by microeukaryotes whereas the COI sequences were dominated by macro-organisms. Each of the 18rDNA primer pairs also exhibited dissimilar community structures although the dominant taxa seemed to be common. To conclude, our results provided a global assessment of tools dedicated to the description of the diversity of marine eukaryotes biofilms from three surfaces used in the design of RME. Among the four extraction methods described here, PowerMaxSoil and PowerBiofilm kits allowed recovering the highest diversity. COI and 18S rDNA gene sequencing covered different groups including at high taxonomic levels. Despite limitations, metabarcoding will help in the characterization of marine biofilms diversity on RME. Especially, it may be relevant to use primers targeting these two genes to better cover the eukaryotic diversity.

Community dissimilarity of angiosperm trees reveals deep‐time diversification across tropical and temperate forests

AbstractQuestionTo better understand the influence of deep‐time diversification on extant plant communities, we assessed how community dissimilarity increases with spatial and climatic distances at multiple taxonomic ranks (species, genus, family, and order) in angiosperm trees. We tested the prediction that the dissimilarity–distance relationship should change across taxonomic ranks depending on the deep‐time diversification in different biogeographical regions reflecting geohistories and geographical settings.LocationGlobal.MethodsUsing a data set of plot‐based surveys across the globe (861 plots), we compiled a community composition matrix comprising 21,455 species, 2,741 genera, 240 families, and 57 orders. We then calculated Sørensen's pairwise dissimilarity (βsor), and its turnover (βsim) and nestedness (βsne) components, among plots within seven biogeographical regions. Finally, we modeled the relationships between the biotic dissimilarities and the spatial/climatic distances at each taxonomic rank, and compared them among regions.Resultsβsor and βsim increased with increasing spatial and climatic distance in all biogeographical regions: βsim was dominant in all biogeographical regions in general, while βsne showed relatively high contributions to total dissimilarity in the temperate regions with historically unstable climatic conditions. The βsim‐distance curve was more saturated at smaller spatial scales in the tropics than in the temperate regions. In general, the curves became flatter at higher taxonomic ranks (order or family), with the exception of Africa, North America, and Australia, pointing to region‐specific geographical constraints.ConclusionsCompositional dissimilarity was generally shaped through the abrupt turnover of species along spatial/climatic gradients. The relatively high importance of the nestedness component in the temperate regions suggests that historical dispersal filters related to extinction/colonization may play important roles. Region‐specific changes in the turnover and nestedness components across taxonomic ranks suggest differential imprints of historical diversification over deep evolutionary time in shaping extant diversity patterns in each biogeographical region.

Contrasting effects of microbial fertiliser and organic fertiliser on soil bacterial community in coal mine dump of Inner Mongolia

ABSTRACT Knowledge about fertiliser limitation to soil microbes is crucial for exploring microbial community succession and ecosystem functions. In this study, an experiment was conducted to promote ecological restoration by different treatments of organic fertiliser (OF), microbial fertiliser (MF) and non-fertiliser (CK) in a coal mine dump. We investigated microbial community structure using high-throughput sequencing. Soils under OF and MF treatment showed distinct community structures with highly bacterial α-diversity due to the variation of soil pH and organic matters (SOM). Of those, the community dissimilarity between OF and CK was higher. The DistLM analysis indicated that SOM and available nitrogen (AN) significantly influenced microbial community structure. Furthermore, functional annotation by the FAPROTAX revealed that the functional groups associating with C, N, and S cycling increased significantly under OF and MF treatment, but decreased that associated with parasites or symbionts. Compared with MF, the functional groups with OF treatment varied greatly. However, the function groups including nitrogen_fixation, hydrocarbon_degradation and methanotrophy were significantly improved under the MF treatment, which have an important implication for soil quality and microbial growth. It was concluded that MF treatment could improve microbial community structure and enhance potential ecosystem function in coal mine dump soils.

Citizens of local jurisdictions enhance plant community preservation through ballot initiatives and voter-driven conservation efforts.

Open space areas protected by local communities may augment larger scale preservation efforts and may offer overlooked benefits to biodiversity conservation provided they are in suitable ecological condition. We examine protected areas established by local communities through ballot initiatives, a form of direct democracy, in California, USA. We compare ecological conditions of wooded habitats on local ballot protected sites and on sites protected by a state-level conservation agency. Collectively, we found few differences in ecological conditions on each protected area type. Ballot sites had greater invasive understory cover and larger trees. Community dissimilarity patterns suggested ballot sites protect a complementary set of tree species to those on state lands. Overall, geographic characteristics influenced onsite conditions more than details of how sites were protected. Thus, community-driven conservation efforts contribute to protected area networks by augmenting protection of some species while providing at least some protection to others that might otherwise be missed.

Fungal and bacterial communities of 'Pinot noir' must: effects of vintage, growing region, climate, and basic must chemistry.

BackgroundThe geographic and temporal distributions of bacterial and fungal populations are poorly understood within the same wine grape cultivar. In this work, we describe the microbial composition from ‘Pinot noir’ must with respect to vintage, growing region, climate, and must chemistry across the states of California and Oregon, USA.Materials and MethodsWe sampled ‘Pinot noir’ clone 667 clusters from 15 vineyards existing in a latitudinal gradient spanning nearly 1,200 km in California and Oregon for two vintages (2016 and 2017). Regions included five American Viticultural Areas (AVA). In order from southern California to Oregon, these AVAs were Santa Barbara, Monterey, Sonoma, Mendocino, and Willamette Valley. Uninoculated grape musts were subjected to 16S rRNA gene and ITS-1 amplicon sequencing to assess composition of microbial communities. We also measured grape maturity metrics. Finally, to describe regions by precipitation and growing degree days, we queried the Parameter-elevation Regressions on Independent Slopes Model (PRISM) spatial climate dataset.ResultsMost of the dominant bacterial taxa in must samples were in the family Enterobacteriaceae, notably the lactic acid bacteria or the acetic acid bacteria groups, but some, like the betaproteobacterial genus Massilia, belonged to groups not commonly found in grape musts. Fungal communities were dominated by Hanseniaspora uvarum (Saccharomycetaceae). We detected relationships between covariates (e.g., vintage, precipitation during the growing season, pH, titratable acidity, and total soluble solids) and bacterial genera Gluconobacter and Tatumella in the family Enterobacteraceae, Sphingomonas (Sphingomonodaceae), Lactobacillus (Lactobacillaceae), and Massilia (Oxalobacteraceae), as well as fungal genera in Hanseniaspora, Kazachstania, Lachancea, Torulaspora in the family Saccharomycetaceae, as well as Alternaria (Pleosporaceae), Erysiphe (Erysiphaceae), and Udeniomyces (Cystofilobasidiaceae). Fungal community distances were significantly correlated with geographic distances, but this was not observed for bacterial communities. Climate varied across regions and vintages, with growing season precipitation ranging from 11 mm to 285 mm and growing degree days ranging from 1,245 to 1,846.DiscussionWe determined that (1) bacterial beta diversity is structured by growing season precipitation, (2) fungal beta diversity reflects growing season precipitation and growing degree days, and (3) microbial differential abundances of specific genera vary with vintage, growing season precipitation, and fruit maturity metrics. Further, the correlation between fungal community dissimilarities and geographic distance suggests dispersal limitation and the vineyard as a source for abundant fungal taxa. Contrasting this observation, the lack of correlation between bacterial community dissimilarity and geographic distance suggests that environmental filtering is shaping these communities.

Accounting for connectivity alters the apparent roles of spatial and environmental processes on metacommunity assembly

Understanding the relative contributions of spatial and environmental processes on community assembly is a central question in ecology. Despite this long-standing interest, our understanding of how landscape structure may drive spatial processes of community assembly remains poorly understood in part because of the challenge of tracking community assembly across landscapes and quantifying key aspects of landscapes that may impact assembly processes. We examined the roles of spatial and environmental processes on structuring assemblies of ants in 72 cleared patches embedded within a forested landscape. To examine the role of spatial processes, we contrasted the use of geographic distances between patches and effective distances estimated from connectivity modeling accounting for matrix vegetation structure hypothesized to be important for ant community assembly. To examine the role of environmental processes, we quantified patch age and abundance of a key competitor and invasive species, the fire ant Solenopsis invicta. We found evidence for the importance of both spatial and environmental processes in structuring ant communities. When spatial processes were quantified as geographic distance, environmental variables were the predominant factors accounting for variation in ant community dissimilarity among patches. However, accounting for matrix resistance with circuit-theoretic connectivity modeling resulted in higher accounting of variation in ant community dissimilarity than geographic distance and changed the predominant variables accounting for that variation from environmental to spatial processes. These findings show that accounting for connectivity through the matrix can be decisive in determining the primary drivers of community assembly.

Changes in assembly processes of soil microbial communities during secondary succession in two subtropical forests

Soil microbes re-establish plant diversity and ecosystem functions after disturbance events. Deterministic and stochastic processes are expected to contribute to microbial community assembly during long-term ecosystem recovery. We characterized soil prokaryotic and fungal communities, to determine their assembly patterns, along two chronosequences with early to later successional subtropical forests. Prokaryotic and fungal community composition was more variable in early successional forests but converged in the later successional forests. The community composition was governed by deterministic processes in the early stages, while the relative influence of stochasticity increased in the later stages. Environmental factors that predicted the shift in deterministic and stochastic balance varied within and across successional stages. In particular, the compositional dissimilarity of plant communities strongly predicted the relative influences of the two processes during succession. These findings suggest that the relative influences of deterministic and stochastic processes in shaping microbial community assembly shift during secondary succession. Consequently, plant communities are important predictors of assembly processes in soil microbial communities during long-term ecosystem recovery.

Self-Crossing Leads to Weak Co-Variation of the Bacterial and Fungal Communities in the Rice Rhizosphere.

The rhizomicrobial community is influenced by plant genotype. However, the potential differences in the co-assembly of bacterial and fungal communities between parental lines and different generations of rice progenies have not been examined. Here we compared the bacterial and fungal communities in the rhizomicrobiomes of female parent Oryza rufipogon wild rice; male parent Oryza sativa cultivated rice; their F1 progeny; and the F2, F3 and F4 self-crossing generations. Our results showed that the bacterial and fungal α-diversities of the hybrid F1 and self-crossing generations (F2, F3, F4) were closer to one of the two parental lines, which may indicate a role of the parental line in the diversity of the rhizosphere microbial community assembly. Self-crossing from F1 to F4 led to weak co-variation of the bacterial and fungal communities and distinct rhizosphere microbiomes. In the parental and self-crossing progenies, the reduction of community dissimilarity was higher for the fungal community than for the bacterial community.

Wine Terroir and the Soil Bacteria: An Amplicon Sequencing-Based Assessment of the Barossa Valley and Its Sub-Regions.

A wines’ terroir, represented as wine traits with regional distinctiveness, is a reflection of both the biophysical and human-driven conditions in which the grapes were grown and wine made. Soil is an important factor contributing to the uniqueness of a wine produced by vines grown in specific conditions. Here, we evaluated the impact of environmental variables on the soil bacteria of 22 Barossa Valley vineyard sites based on the 16S rRNA gene hypervariable region 4. In this study, we report that both dispersal isolation by geographic distance and environmental heterogeneity (soil plant-available P content, elevation, rainfall, temperature, spacing between row and spacing between vine) contribute to microbial community dissimilarity between vineyards. Vineyards located in cooler and wetter regions showed lower beta diversity and a higher ratio of dominant taxa. Differences in soil bacterial community composition were significantly associated with differences in fruit and wine composition. Our results suggest that environmental factors affecting wine terroir, may be mediated by changes in microbial structure, thus providing a basic understanding of how growing conditions affect interactions between plants and their soil bacteria.

Arctic insect emergence timing and composition differs across thaw ponds of varying morphology

ABSTRACT Freshwater ponds provide habitats for aquatic insects that emerge and subsidize consumers in terrestrial ecosystems. In the Arctic, insects provide an important seasonal source of energy to birds that breed and rear young on the tundra. The abundance and timing of insect emergence from arctic thaw ponds is poorly understood, but understanding these fluxes is important, given the role of insects in food webs and current rates of environmental change at high latitudes. We aimed to evaluate emerging insect communities from thaw ponds with different morphologies, identify environmental covariates influencing insect composition, and describe temporal changes in insect abundance. We collected environmental information and insects that emerged over two growing seasons and examined the phenology and taxonomic composition of insects arising from different pond classes: low centered polygon, small coalescent, large coalescent, and trough ponds. Our findings indicated no differences in the timing of total emergence across ponds of varying morphology. Community dissimilarity was primarily associated with center or margin habitat and variables that differed strongly among pond classes. These insects, which provide important provisions for various species of birds, are likely to experience changes in emergence phenology and composition due to ongoing, rapid warming in the region.

Impact of dominants on the species richness and compositional dissimilarity of high mountain plant communities of the Western Caucasus (Caucasian State Nature Reserve, Russia)

Impact of dominants on the species richness and compositional dissimilarity of high mountain plant communities of the Western Caucasus (Caucasian State Nature Reserve, Russia)

Spatio-temporal variability of Brachyura larval assemblages in mangroves of the Gulf of Guayaquil’s inner estuary

Mangroves are the dominant coastal vegetation in tropical estuaries and host a large diversity of brachyuran crabs. Crab larvae have adapted to dynamic hydrological conditions in estuaries using several physiological and behavioral strategies. Changes in crab larval assemblages can be monitored in time in order to detect ecological changes occurring within estuaries. For this study, we sampled quarterly crab larval assemblages in two sub-estuaries (Salado and Churute) of the Gulf of Guayaquil (GG) during 2016–2017. The largest community dissimilarities occurred between sub-estuaries, with Salado having higher morphological diversity and larval densities than Churute. Temporal patterns were only evident within each sub-estuary, and in relation to total and individual morpho-species density values. Ocypodidae larvae were dominant across samples; with zoea I of the red mangrove crab (Ucides occidentalis) showing maximal density values during spring tides. Hydrological parameters (i.e., turbidity, conductivity, salinity and temperature) contributed to only 19% of the variability in biota, demonstrating that crab larvae are physiologically adapted to a wide range of water conditions. This study established an ecological baseline for future studies using crab larval assemblages in the assessment of ecological changes occurring in mangrove tidal creeks of the GG. However, longer time-series monitoring data and description of new species and stages of crab larvae are necessary to better assess potential future changes.

Metataxonomic profiling of bacterial communities and their predictive functional profiles in traditionally preserved meat products of Sikkim state in India

Traditionally preserved meat products are common food items in Sikkim state of India. We studied the high-throughput sequencing of four traditionally preserved meat products viz. beef kargyong, pork kargyong, yak satchu and khyopeh to profile the bacterial communities and also inferred their predictive functional profiles. Overall abundant OTUs in samples showed that Firmicutes was the abundant phylum followed by Proteobacteria and Bacteroidetes. Abundant species detected in each product were Psychrobacter pulmonis in beef kargyong, Lactobacillus sakei in pork kargyong, Bdellovibrio bacteriovorus and Ignatzschinera sp. in yak satchu and Lactobacillus sakei and Enterococcus sp. in khyopeh. Several genera unique to each product, based on analysis of shared OTUs contents, were observed among the samples except in khyopeh. Goods coverage recorded to 1.0 was observed, which reflected the maximum bacterial diversity in the samples. Alpha diversity metrics showed a maximum bacterial diversity in khyopeh and lowest in pork kargyong Community dissimilarities in the products were observed by PCoA plot. A total of 133 KEGG predictive functional pathways was observed in beef kargyong, 131 in pork kargyong, 125 in yak satchu and 101 in khyopeh. Metagenome contribution of the OTUs was computed using PICTRUSt2 and visualized by BURRITO software to predict the metabolic pathways. Several predictive functional profiles were contributed by abundant OTUs represented by Enterococcus, Acinetobacter, Agrobacterium, Bdellovibrio, Chryseobacterium, Lactococcus, Leuconostoc, Psychrobacter, and Staphylococcus.

Quantitative evaluation of species composition dissimilarity within a community and among communities

AbstractIt is often necessary to perform quantitative comparisons and assessments of species composition among plant communities under various land use conditions and landscapes, as well as among plant communities at different stages of restoration or degradation in arid grasslands. In landscapes composed of a number of plant communities, in which many quadrats for a survey are set in each community, the species composition in each quadrat is measured using community variables, such as the presence/absence data (i.e., binary variable), biomass, cover, the number of individuals, or the frequency of occurrences (i.e., quantitative variables) of each species per quadrat. In this study, we defined two types of species composition dissimilarity in vegetation surveys: between different communities and within each community which were calculated based on the species composition of each quadrat, using the Bray–Curtis index. The second type dissimilarity occurs incidentally among quadrats (or micro‐sites) even in a community with a relatively uniform structure. Both dissimilarity measures take values from 0 to 1, where larger values indicate larger dissimilarities, and the quadrat‐to‐quadrat variation in dissimilarity also indicates the degree of heterogeneity in the spatial pattern of species composition. Quantifying dissimilarity between and within communities remains a challenge in ecological applications. We proposed a new model to quantify community dissimilarity and applied this model to a grassland vegetation survey dataset. Quantitative variables resulted in more precise measures of community structure than binary variable. The advantages of our model relative to other broadly used community structure metrics based on the Jaccard and Sørensen indices were discussed.

Vegetation richness, species identity and soil nutrients drive the shifts in soil bacterial communities during restoration process.

Soil bacteria play an essential role in functioning of ecosystems and maintaining of biogeochemical cycles. However, little is known about changes in the compositions and functional groups of soil bacterial communities during different restoration stages. The influences of aboveground vegetation and belowground soil properties on soil bacterial communities were also unclear during this process. Here we sequenced the soil bacterial communities in different stages of sand fixation. Sand fixation increased the diversity of the bacterial communities, among which the populations of Actinobacteria, Acidobacteria and Gemmatimonadetes changed significantly. The function prediction showed sand fixation increased Gram-positive and aerobic bacteria. Bacterial structure is significantly correlated with plant richness, coverage and biomass. In particular, we found species identity was an important determinant in structuring bacterial composition. Soil properties were all significantly correlated with soil bacterial community richness and diversity. Fusobacteria was strongly positively correlated with sand, Chloroflexi with total N and Gemmatimonadetes with SOM and total C. It suggested that soil nutrients (TC, TN and SOM) have large consequences for soil bacterial community dissimilarities. These results indicated that vegetation richness, especially species identity, together with improvement in soil nutrients, play key roles in driving the shifts in soil microbial community structure and function during restoration process.

Controls on diatom biogeography on South Carolina (USA) barrier island beaches

Benthic microalgae are of great significance to coastal productivity and nutrient cycling, yet determinants of their biogeography and community assembly remain unclear. We identified and compared spatial and environmental mechanisms that shape beach diatom biogeography and diversity at regional scales. We sampled at various spatial scales (from 10 cm to 120 km) from 4 barrier island beaches in South Carolina, USA, and characterized diatom assemblages using DNA metabarcoding. Twelve environmental variables from sediments, adjacent waters, and atmosphere were recorded. Despite attempts to sample from similar habitat types, environmental factors varied among islands. Correspondingly, biomass and α-diversity metrics likewise varied and were positively related to sediment nutrient levels. Community composition also varied, with each island dominated by different diatom taxa. Redundancy analysis revealed that spatial influences, in addition to environmental factors (water temperature and porewater nutrients), were significantly related to community dissimilarity (β-diversity). Variation partitioning attributed only ~5% of community variation to geographic distance alone, whereas 22% was explained by combined spatial/environmental factors. A high proportion (73%) of community dissimilarity remained unexplained, which likely implicates stochastic processes, although unmeasured physico-chemical or biological factors cannot be discounted. Weak spatial effects suggest that dispersal limitation was relatively unimportant, likely due to extensive sediment transport between beaches. Instead, spatially structured environmental variables appeared to condition beach diatom biogeography. These findings broaden our understanding of microbial biogeography to less well-studied microorganisms and marine habitats. More practically, results suggest some degree of predictability in diatom community changes in the face of anthropogenic challenges.

Land use and local environment affect macroinvertebrate metacommunity organization in Neotropical stream networks

AbstractAimChanges in land use and cover (hereafter land use) affect freshwater ecosystems at different spatial scales. We tested the effects of land use on the dispersal capacity of stream macroinvertebrates through local and regional processes.LocationIn all, 183 Brazilian headwater stream sites, located in the Neotropical Savanna with variable land use and covering a total area of 46,394 km2.TaxonStream macroinvertebratesMethodsWe used multiple regression models for distance matrices to identify the relative importance of environmental and landscape characteristics to explain community dissimilarity of stream macroinvertebrates with different mobility traits. As predictors, we calculated four distance metrics: environmental distance describing the dissimilarity in local conditions, the network distance accounting for distances across the drainage system and two distances measuring landscape resistance to dispersal (topographic and land use). We classified macroinvertebrates in dispersal groups according to their dispersal abilities (flying and drifting) and life story traits (voltinism, adult life span and body size). We tested the effects of these distances on all taxa and on the different dispersal groups, to explore whether biological traits would result in different metacommunity patterns.ResultsOur hierarchical clustering analysis identified five macroinvertebrate dispersal groups. The dispersal group 1 was mainly composed by aquatic obligate taxa, dispersal group 2 by taxa with low drift propensity, dispersal group 3 represented taxa with high directional flight capacity, dispersal group 4 included taxa with medium drift propensity and dispersal group 5 represented taxa with high drift propensity. We found that environmental distance and land use distance were the most important predictors explaining community dissimilarity for most of the dispersal groups.Main conclusionThe metacommunity patterns found in this study suggest that environmental filtering was the most important community assembly mechanism at a local scale, whereas land use could constrain dispersal at the regional scale. Understanding these processes is crucial to meet conservation and restoration goals, especially in biodiversity hotspots. Our results reinforce the importance of considering entire catchments for preserving stream health and aquatic biodiversity and indicate the need for a much more integrative research between terrestrial and aquatic ecology.

Stream Microbial Community Structured by Trace Elements, Headwater Dispersal, and Large Reservoirs in Sub-Alpine and Urban Ecosystems.

Stream bacterioplankton communities, a crucial component of aquatic ecosystems and surface water quality, are shaped by environmental selection (i.e., changes in taxa abundance associated with more or less favorable abiotic conditions) and passive dispersal (i.e., organisms’ abundance and distribution is a function of the movement of the water). These processes are a function of hydrologic conditions such as residence time and water chemistry, which are mediated by human infrastructure. To quantify the role of environmental conditions, dispersal, and human infrastructure (dams) on stream bacterioplankton, we measured bacterioplankton community composition in rivers from sub-alpine to urban environments in three watersheds (Utah, United States) across three seasons. Of the 53 environmental parameters measured (including physicochemical parameters, solute concentrations, and catchment characteristics), trace element concentrations explained the most variability in bacterioplankton community composition using Redundancy Analysis ordination. Trace elements may correlate with bacterioplankton due to the commonality in source of water and microorganisms, and/or environmental selection creating more or less favorable conditions for bacteria. Bacterioplankton community diversity decreased downstream along parts of the stream continuum but was disrupted where large reservoirs increased water residence time by orders of magnitude, potentially indicating a shift in the relative importance of environmental selection and dispersal at these sites. Reservoirs also had substantial effects on community composition, dissimilarity (Bray-Curtis distance) and species interactions as indicated by co-occurrence networks. Communities downstream of reservoirs were enriched with anaerobic Sporichthyaceae, methanotrophic Methylococcaceae, and iron-transforming Acidimicrobiales, suggesting alternative metabolic pathways became active in the hypolimnion of large reservoirs. Our results identify that human activity affects river microbial communities, with potential impacts on water quality through modified biogeochemical cycling.

Foliar fungal endophyte community structure is independent of phylogenetic relatedness in an Asteraceae common garden.

Phylogenetic distance among host species represents a proxy for host traits that act as biotic filters to shape host‐associated microbiome community structure. However, teasing apart potential biotic assembly mechanisms, such as host specificity or local species interactions, from abiotic factors, such as environmental specificity or dispersal barriers, in hyperdiverse, horizontally transmitted microbiomes remains a challenge. In this study, we tested whether host phylogenetic relatedness among 18 native Asteraceae plant species and spatial distance between replicated plots in a common garden affects foliar fungal endophyte (FFE) community structure. We found that FFE community structure varied significantly among host species, as well as host tribes, but not among host subfamilies. However, FFE community dissimilarity between host individuals was not significantly correlated with phylogenetic distance between host species. There was a significant effect of spatial distance among host individuals on FFE community dissimilarity within the common garden. The significant differences in FFE community structure among host species, but lack of a significant host phylogenetic effect, suggest functional differences among host species not accounted for by host phylogenetic distance, such as metabolic traits or phenology, may drive FFE community dissimilarity. Overall, our results indicate that host species identity and the spatial distance between plants can determine the similarity of their microbiomes, even across a single experimental field, but that host phylogeny is not closely tied to FFE community divergence in native Asteraceae.

Determinants of bacterioplankton structures in the typically turbid Weihe River and its clear tributaries from the northern foot of the Qinling Mountains

The Weihe River is the largest tributary of the typically sediment-laden Yellow River in China. Assuming that high sediment concentrations may increase the turbidity of water bodies, and therefore affect riverine ecosystem, in which the bacterioplankton are crucial components and serve as important indicators of environmental and ecological status through their structure and response to the environment change, it is essential to deep understanding the bacterioplankton structure and influencing factors in turbid and clear river ecosystems. Here, high-throughput sequencing was used to analyze the differences in bacterioplankton structure and major determinants in the typically turbid Weihe River and its clear tributaries from the northern foot of the Qinling Mountains from October to November 2017 and April to May 2018. The results demonstrated that bacterioplankton communities shared similar dominant subcommunities in the Weihe River mainstem and its tributaries, mainly consisting of Proteobacteria and Bacteroidetes phyla and Flavobacterium and Acinetobacter genera. The Faith phylogenetic diversity (PD) index was significantly higher in the turbid mainstem than in the tributaries and was related to turbidity (Turb). Variation partitioning analysis (VPA) showed that geographical distance exhibited notable influences on the community composition in the mainstem; however, the communities in the tributaries had a much stronger response to local environmental factors. Bacteria exhibited a significant distance-decay relationship in the mainstem, whereas geographical distance was not correlated with community dissimilarities in the tributaries. Chlorophyll a emerged as the major determinant of the bacterioplankton structure in the turbid Weihe River, indicating the importance of phytoplankton-bacterioplankton relationships in the turbid river system. These results provide important insights into future research on microbial ecology, environmental monitoring and classified management in diverse river systems.