Effects of Cascade Reservoirs on Spatiotemporal Dynamics of the Sedimentary Bacterial Community: Co-occurrence Patterns, Assembly Mechanisms, and Potential Functions

Dam construction as an important anthropogenic activity significantly influences ecological processes in altered freshwater bodies. However, the effects of multiple cascade dams on microbial communities have been largely overlooked. In this study, the spatiotemporal distribution, co-occurrence relationships, assembly mechanisms, and functional profiles of sedimentary bacterial communities were systematically investigated in 12 cascade reservoirs across two typical karst basins in southwest China over four seasons. A significant spatiotemporal heterogeneity was observed in bacterial abundance and diversity. Co-occurrence patterns in the Wujiang Basin exhibited greater edge counts, graph density, average degree, robustness, and reduced modularity, suggesting more intimate and stronger ecological interactions among species than in the Pearl River Basin. Furthermore, Armatimonadota and Desulfobacterota, identified as keystone species, occupied a more prominent niche than the dominant species. A notable distance-decay relationship between geographical distance and community dissimilarities was identified in the Pearl River Basin. Importantly, in the Wujiang Basin, water temperature emerged as the primary seasonal variable steering the deterministic process of bacterial communities, whereas 58.5% of the explained community variance in the neutral community model (NCM) indicated that stochastic processes governed community assembly in the Pearl River Basin. Additionally, principal component analysis (PCA) revealed more pronounced seasonal dynamics in nitrogen functional compositions than spatial variation in the Wujiang Basin. Redundancy analysis (RDA) results indicated that in the Wujiang Basin, environmental factors and in Pearl River Basin, geographical distance, reservoir age, and hydraulic retention time (HRT), respectively, influenced the abundance of nitrogen-related genes. Notably, these findings offer novel insights: building multiple cascade reservoirs could lead to a cascading decrease in biodiversity and resilience in the river-reservoir ecosystem.

Unraveling the antibiotic resistome in backwater zones of large cascade reservoirs: Co-occurrence patterns, horizontal transfer directions and health risks

The widespread occurrence of antibiotic resistant genes (ARGs) throughout aquatic environments has raised global concerns for public health. However, the profiles and patterns of antibiotic resistome in backwater zone of cascade reservoirs, where water flow is slowed down, are still poorly understood. Here, we proposed a metagenomic analysis framework to comprehensively reveal the diversity, abundance, co-occurrence patterns and transfer direction of ARGs in cascade reservoirs system and evaluated their health risks through a procedure based on contigs. A total of 364 ARGs subtypes conferring resistance to different antibiotics classes were detected in our water samples, and the dominant ARGs (macB, bacA, vanRA, bcrA) were similar in different reservoirs. Meanwhile, the distribution of ARGs was influenced by the presence of biotic factors such as metal resistant genes (MRGs) and mobile genetic elements (MGEs), as well as abiotic factors such as dissolved oxygen (DO) and pH. Remarkably, ARGs (vanR, rosB, MexT) co-occurred with plasmids and virulence factor genes (VFGs), which can lead to the emergence and spread of highly virulent and antibiotic resistant bacteria in microbial communities. Overall, this study helps administrators to better understand the complex patterns of ARGs in backwater zones of large cascade reservoirs and provides a proper procedure for detecting the presence of high-risk of ARGs.

Cd contamination determined assembly processes and network stability of AM fungal communities in an urban green space ecosystem

The effects of cadmium (Cd) contamination on the assembly mechanism and co-occurrence patterns of arbuscular mycorrhizal (AM) fungal communities remain unclear, especially in urban green spaces. This study sequenced AM fungal communities in greenbelt soils in Zhengzhou (China). The effects of Cd contamination on the AM fungal diversity, community assembly processes, and co-occurrence patterns were explored. We found that (1) an increase in Cd contamination changed the community composition, which resulted in a significant improvement in the diversity of specialists of AM fungi and a significant decrease in the diversity of generalists. (2) Deterministic processes dominated the community assembly of specialists and stochastic processes dominated the community assembly of generalists. (3) Specialists played a more important role than generalists in maintaining the stability of AM fungal networks under Cd contamination. Overall, Cd contamination affected the ecological processes of AM fungi in urban green space ecosystems. However, the effects on the assembly processes and network stability of different AM fungi taxa (specialists and generalists) differed significantly. The present study provides deeper insight into the effect of Cd contamination on the ecological processes of AMF and is helpful in further exploring the ecological risk of Cd contamination in urban green spaces.

Deciphering the degradation characteristics of the fungicides imazalil and penflufen and their effects on soil bacterial community composition, assembly, and functional profiles

The adsorption-desorption and degradation characteristics of two widely applied fungicides, imazalil and penflufen, and the responses of soil bacterial diversity, structure, function, and interaction after long-term exposure were systemically studied in eight different soils. The adsorption ability of imazalil in soil was significantly higher than that of penflufen. Both imazalil and penflufen degraded slowly in most soils following the order: imazalil > penflufen, with soil pH, silt, and clay content being the potential major influencing factors. Both imazalil and penflufen obviously inhibited the soil microbial functional diversity, altered the soil bacterial community and decreased its diversity. Although exposure to low and high concentrations of imazalil and penflufen strengthened the interactions among the soil bacterial communities, the functional diversity of the co-occurrence network tended to be simple at high concentrations, especially in penflufen treatment. Both imazalil and penflufen markedly disturbed soil nitrogen cycling, especially penflufen seriously inhibited most nitrogen cycling processes, such as nitrogen fixation and nitrification. Meanwhile, sixteen and ten potential degradative bacteria of imazalil and penflufen, respectively, were found in soils, including Kaistobacter and Lysobacter. Collectively, the long-term application of imazalil and penflufen could cause residual accumulation in soils and subsequently result in serious negative effects on soil ecology.

Fertilizing-induced alterations of microbial functional profiles in soil nitrogen cycling closely associate with crop yield

Fertilization and rhizosphere selection are key regulators for soil nitrogen (N) cycling and microbiome. Thus, clarifying how the overall N cycling processes and soil microbiome respond to these factors is a prerequisite for understanding the consequences of high inputs of fertilizers, enhancing crop yields, and formulating reasonable nitrogen management strategies under agricultural intensification scenarios. To do this, we applied shotgun metagenomics sequencing to reconstruct N cycling pathways on the basis of abundance and distribution of related gene families, as well as explored the microbial diversity and interaction via high throughput sequencing based on a two-decade fertilization experiment in Loess Plateau of China semiarid area. We found that bacteria and fungi respond divergent to fertilization regimes and rhizosphere selection, in terms of community diversity, niche breadth, and microbial co-occurrence networks. Moreover, organic fertilization decreased the complexity of bacterial networks but increased the complexity and stability of fungal networks. Most importantly, rhizosphere selection exerted more strongly influences on the soil overall nitrogen cycling than the application of fertilizers, accompanied by the increase in the abundance of nifH, NIT-6, and narI genes and the decrease in the abundance of amoC, norC, and gdhA genes in the rhizosphere soil. Furthermore, keystone families screening from soil microbiome (e.g., Sphingomonadaceae, Sporichthyaceae, and Mortierellaceae), which were affected by the edaphic variables, contributed greatly to crop yield. Collectively, our findings emphasize the pivotal roles of rhizosphere selection interacting with fertilization regimes in sustaining soil nitrogen cycling processes in response to decades-long fertilization, as well as the potential importance of keystone taxa in maintaining crop yield. These findings significantly facilitate our understanding of nitrogen cycling in diverse agricultural soils and lay a foundation for manipulating specific microorganisms to regulate N cycling and promote agroecosystem sustainability.

Actinobacteria produce taste and odor in drinking water reservoir: Community composition dynamics, co-occurrence and inactivation models

Taste and odor (T&O) has become a significant concern for drinking water safety. Actinobacteria are believed to produce T&O during the non-algal bloom period; however, this has not been widely investigated. In this study, the seasonal dynamics of the actinobacterial community structure and inactivation of odor-producing actinobacteria were explored. The results indicated that the diversity and community composition of actinobacteria exhibited significant spatiotemporal distribution. Network analysis and structural equation modeling showed that the actinobacterial community occupied a similar environmental niche, and the major environmental attributes exhibited spatiotemporal dynamics, which affected the actinobacterial community. Furthermore, the two genera of odorous actinobacteria were inactivated in drinking water sources using chlorine. Amycolatopsis spp. have a stronger chlorine resistance ability than Streptomyces spp., indicating that chlorine inactivates actinobacteria by first destroying cell membranes and causing the release of intracellular compounds. Finally, we integrated the observed variability in the inactivation rate of actinobacteria into an expanded Chick-Watson model to estimate its effect on inactivation. These findings will deepen our understanding of the seasonal dynamics of actinobacterial community structure in drinking water reservoirs and provide a foundation for reservoir water quality management strategies.

Distinct community assembly processes and habitat specialization driving the biogeographic patterns of abundant and rare bacterioplankton in a brackish coastal lagoon

The ecological diversity patterns and community assembly processes along spatio-temporal scales are least studied in the bacterioplankton sub-communities of brackish coastal lagoons. We examined the biogeographic patterns and relative influences of different assembly processes in structuring the abundant and rare bacterioplankton sub-communities of Chilika, the largest brackish water coastal lagoon of India. Rare taxa demonstrated significantly higher α- and β-diversity and biogeochemical functions than abundant taxa in the high-throughput 16S rRNA gene sequence dataset. The majority of the abundant taxa (91.4 %) were habitat generalists with a wider niche breadth (niche breadth index, B = 11.5), whereas most of the rare taxa (95.2 %) were habitat specialists with a narrow niche breadth (B = 8.9). Abundant taxa exhibited a stronger distance-decay relationship and higher spatial turnover rate than rare taxa. β-diversity partitioning revealed that the contribution of species turnover (72.2-97.8 %) was greater than nestedness (2.2-27.8 %) in causing the spatial variation in both abundant and rare taxa. Null model analyses revealed that the distribution of abundant taxa was mostly structured by stochastic processes (62.8 %), whereas deterministic processes (54.1 %) played a greater role in the rare taxa. However, the balance of these two processes varied across spatio-temporal scales in the lagoon. Salinity was the key deterministic factor controlling the variation of both abundant and rare taxa. Potential interaction networks showed a higher influence of negative interactions, indicating that species exclusion and top-down processes played a greater role in the community assembly. Notably, abundant taxa emerged as keystone taxa across spatio-temporal scales, suggesting their greater influences on other bacterial co-occurrences and network stability. Overall, this study provided detailed mechanistic insights into biogeographic patterns and underlying community assembly processes of the abundant and rare bacterioplankton over spatio-temporal scales in a brackish lagoon.

Copper and temperature shaped abundant and rare community assembly respectively in the Yellow River

Untangling assembly and microbial interaction of abundant and rare microbiota in aquatic ecosystem is pivotal for understanding how community assembly respond to environmental variables and co-occurrence patterns. Here, we explored the assembly mechanisms, their drivers, and species co-occurrence of abundant and rare microbiomes in the Yellow River using 16S rRNA gene sequencing in Lanzhou, China. Here, abundant community was ubiquitous across all sites, whereas rare community was uneven distributed. The richness and community dissimilarity of rare taxa were significantly greater than those of abundant ones. Stochastic processes structured the rare community assembly in spring and winter, while deterministic processes shaped the abundant and rare community assembly in other seasons and all sites. Copper and water temperature mediated the balance between deterministic and stochastic processes of abundant and rare community, respectively. A few abundant taxa with closer relationships frequently occupied central positions and had a great effect on other co-occurrences in the network, while the majority of keystone microbiota were rare microbiome and played a considerable part in maintaining the network structure. Our study provides some ecological proposals for water quality management and ecological stability of the Yellow River. KEY POINTS: • Deterministic process dominated abundant and rare community assembly. • Cu and TW mediated the balance of abundant and rare community assembly respectively. • Abundant taxa had a greater effect on other co-occurrences in the network.

Different ratios of raw material triggered composting maturity associated with bacterial community co-occurrence patterns

Exploring the ecological function of potential core bacteria for high-efficiency composting can provide a fundamental understanding of the role of composting bacterial communities. Mushroom residue and kitchen garbage at different ratios (N1: 1/1, N2: 1/2) of dry weight were tested to investigate the key ecological role of the core bacteria responsible for producing mature compost. N1 had a peak temperature of 75.0 °C which was higher than N2 (68.3 °C). Other key composting parameters (carbon to nitrogen ratio (C/N) and germination index (GI)) also indicated that N1 achieved higher compost maturity. Rice seedlings experiments also further validated this conclusion. Putative key bacterial taxa (Thermobifida, Luteimonasd, Bacillus, etc.) were positively associated with the GI, indicating a substantial contribution to composting maturity. Co-occurrence network analysis revealed the ecological function of potentially beneficial core bacteria promoted cooperation among the bacterial community. The putative core bacteria in N1 may affect composting efficiency. Our findings reveal the mechanism of potential core bacteria throughout the compost maturity phases.

Active tailings disturb the surrounding vegetation soil fungal community: Diversity, assembly process and co-occurrence patterns

Soil fungi play an important role in the soil biogeochemical cycle and are important biological indicators for the ecological remediation of mine tailings contaminated sites, therefore understanding the characteristics of soil fungal communities is a key aspect of pollution remediation. However, the influence of biological factors on the characteristics of fungal community diversity; assembly mechanisms and co-occurrence patterns of fungal community along environmental gradients around tailings are not well understood. In this study, soil samples from forest, agriculture and grass around tailings were collected to reveal the assembly mechanisms and co-occurrence patterns of soil fungal community and to quantify the contribution of abiotic and biotic factors to fungal diversity. The results suggest that vegetation types and Cu concentration together drive the distribution of fungal diversity. We found that Exophiala has potential as a biomarker species indicative of restoration progress. Increased environmental stress accelerates the process of changing fungal community assemblages from stochastic to deterministic, while also allowing fungal communities tend to resist tailings-induced environmental stresses through species coexistence. Together, this study provides new insights into the influence of biological factors on fungal community diversity, as well as revealing mechanisms of fungal community assembly and co-occurrence patterns, which are important for understanding the maintenance mechanisms of fungal community diversity and ecological remediation of tailings-contaminated soils.

Response mechanism of meiofaunal communities to multi-type of artificial reef habitats from the perspective of high-throughput sequencing technology

Multiple types of artificial reefs have been widely deployed in the coast of northern Yellow Sea, which can enhance fishery resources, restore coastal habitats and improve the marine environment. Meiofauna plays important ecological roles in marine ecosystem, but the response mechanism of meiofaunal community to different types of artificial reef is still poorly understood. In this study, we characterized the meiofaunal communities of concrete artificial reef habitat (CAR), rocky artificial reef habitat (RAR), ship artificial reef habitat (SAR) and adjacent natural habitat (NH) using 18S rRNA gene high-throughput sequencing technology, and explored the relationship of community-environment. The results showed that the diversity and community structure of meiofauna differed significantly on both spatial and temporal scales. Spatial differences were mainly contributed to the flow field effects and biological effects generated by artificial habitats, while temporal differences were driven by temperature (T) and dissolved oxygen (DO). The dominant taxa of meiofauna included arthropods, annelids, platyhelminths and nematodes. Platyhelminths were mainly positively influenced by artificial habitats but annelids were the opposite. Co-occurrence network analysis revealed that NH was more sensitive to environmental change than artificial habitat, while the performance of CAR and SAR were more stable. These results indicated that meiofauna can respond accordingly to different types of artificial habitats, and could be superimposed over the normal seasonal effects. The current study could provide fundamental data for understanding the response mechanism of meiofaunal community to different types of artificial habitats and a reference for assessments of the impact of artificial reefs on the marine environment.

Spatiotemporal Dynamics of Bacterial Taxonomic and Functional Profiles in Estuarine Intertidal Soils of China Coastal Zone

Bacteria play an important role in regulating carbon (C), nitrogen (N), and sulfur (S) in estuarine intertidal wetlands. To gain insights into the ecological and metabolic modes possessed by bacteria in estuarine intertidal wetlands, a total of 78 surface soil samples were collected from China's coastal intertidal wetlands to examine the spatial and seasonal variations of bacterial taxonomic composition, assembly processes, and ecological system functions through shotgun metagenomic and 16S rRNA gene sequencing. Obvious spatiotemporal dynamic patterns in the bacterial community structure were identified, with more pronounced seasonal rather than spatial variations. Dispersion limitation was observed to act as a critical factor affecting community assembly, explaining approximately half of the total variation in the bacterial community. Functional bacterial community structure exhibited a more significant latitudinal change than seasonal variability, highlighting that functional stability of the bacterial communities differed with their taxonomic variability. Identification of biogeochemically related links between C, N, and S cycles in the soils showed the adaptive routed metabolism of the bacterial communities and the strong interactions between coupled metabolic pathways. Our study broadens the insights into the taxonomic and functional profiles of bacteria in China's estuarine intertidal soils and helps us understand the effects exerted by environmental factors on the ecological health and microbial diversity of estuarine intertidal flats.

Temporal Succession of Bacterial Community Structure, Co-occurrence Patterns, and Community Assembly Process in Epiphytic Biofilms of Submerged Plants in a Plateau Lake

In shallow macrophytic lakes, epiphytic biofilms are formed on the surface of submerged plant stems and leaves because of algae and bacterial accumulation. Epiphytic biofilms significantly impact the health of the host vegetation and the biogeochemical cycling of lake elements. However, community diversity, species interactions, and community assembly mechanisms in epiphytic bacterial communities (EBCs) of plants during different growth periods are not well understood. We investigated the successional dynamics, co-occurrence patterns, and community assembly processes of epiphytic biofilm bacterial communities of submerged plants, Najas marina and Potamogeton lucens, from July to November 2020. The results showed a significant seasonal variation in EBC diversity and richness. Community diversity and richness increased from July to November, and the temperature was the most important driving factor for predicting seasonal changes in EBC community structure. Co-occurrence network analysis revealed that the average degree and graph density of the network increased from July to November, indicating that the complexity of the EBC network increased. The bacterial community co-occurrence network was limited by temperature, pH, and transparency. The phylogeny-based null model analysis showed that deterministic processes dominated the microbial community assembly in different periods, increasing their contribution. In addition, we found that as the dominance of deterministic processes increased, the microbial co-occurrence links increased, and the potential interrelationships between species became stronger. Thus, the findings provide insights into the seasonal variability of EBC assemblage and co-occurrence patterns in lacustrine ecosystems.

Variation in community structure and network characteristics of spent mushroom substrate (SMS) compost microbiota driven by time and environmental conditions

Global mushroom production is growing rapidly, raising concerns about polluting effects of spent mushroom substrate (SMS) and interest in uses in composts. In this study, SMS composting trials and high-throughput sequencing were carried out to investigate to better understand how the structure, co-occurrence patterns, and functioning of bacterial and fungal communities vary through compost time and across environmental conditions. The results suggested that both bacterial and fungal microbiota displayed significant variation in community composition across different composting stages. Enzyme activity levels showed both directional and fluctuating changes during composting, and the activity dynamics of carboxymethyl cellulase, polyphenol oxidase, laccase, and catalase correlated significantly with the succession of microbial community composition. The co-occurrence networks are "small-world" and modularized and the topological properties of each subnetwork were significantly influenced by the environmental factors. Finally, seed germination and seedling experiments were performed to verify the biosafety and effectiveness of the final composting products.

New insights into cyanobacterial blooms and the response of associated microbial communities in freshwater ecosystems

Cyanobacterial blooms are important environmental problems in aquatic ecosystems. Researchers have found that cyanobacterial blooms cannot be completely prevented by controlling and/or eliminating pollutants (nutrients). Thus, more in-depth basic research on the mechanism of cyanobacterial blooms is urgently needed. Cyanobacteria, being primordial microorganisms, provide habitats and have various forms of interactions (reciprocity and competition) with microorganisms, thus having a significant impact on themselves. However, little is known about how environmental conditions and microbial communities in both water and sediment jointly affect cyanobacterial blooms or about the co-occurrence patterns and interactions of microbial communities. We investigated changes in environmental factors and microbial communities in water and sediment during different cyanobacterial blooms and revealed their interacting effects on cyanobacteria. Cyanobacteria had greater competitive and growth advantages than other microorganisms and had antagonistic and aggressive effects on them when resources (such as nutrients) were abundant. Furthermore, microbial networks from cyanobacterial degradation periods may be more complex and stable than those from bloom periods, with more positive links among the microbial networks, suggesting that microbial community structures strengthen interconnections with each other to degrade cyanobacteria. In addition, we found that sediment-enriched cyanobacteria play a key role in cyanobacterial blooms, and sediment microorganisms promote the nutrient release, further promoting cyanobacterial blooms in the water bodies. The study contributes to further our understanding of the mechanisms for cyanobacterial blooms and microbial community structural composition, co-occurrence patterns, and responses to cyanobacteria. These results can contribute to future management strategies for controlling cyanobacterial blooms in freshwater ecosystems.

Horizontal transfer of antibiotic resistance genes within the bacterial communities in aquacultural environment

Very little is known about how microbiome interactions shape the horizontal transfer of antibiotic resistance genes in aquacultural environment. To this end, we first conducted 16S rRNA gene amplicon sequencing to monitor the dynamics of bacterial community compositions in one shrimp farm from 2019 to 2020. Next, co-occurrence analysis was then conducted to reveal the interactions network between Vibrio spp. and other species. Subsequently, 21 V. parahaemolyticus isolates and 15 related bacterial species were selected for whole-genome sequencing (WGS). The 16S rDNA amplicon sequencing results identified a remarkable increase of Vibrio and Providencia in September-2019 and a significant rise of Enterobacter and Shewanella in Septtember-2020. Co-occurrence analysis revealed that Vibrio spp. positively interacted with the above species, leading to the sequencing of their isolates to further understand the sharing of the resistant genomic islands (GIs). Subsequent pan-genomic analysis of V. parahaemolyticus genomes identified 278 horizontally transferred genes in 10 GIs, most of which were associated with antibiotic resistance, virulence, and fitness of metabolism. Most of the GIs have also been identified in Providencia, and Enterobacter, suggesting that exchange of genetic traits might occur in V. parahaemolyticus and other cooperative species in a specific niche. No genetic exchange was found between the species with negative relationships. The knowledge generated from this study would greatly improve our capacity to predict and mitigate the emergence of new resistant population and provide practical guidance on the microbial management during the aquacultural activities.

Nitrogen rather than phosphorus driving the biogeographic patterns of abundant bacterial taxa in a eutrophic plateau lake

Eutrophication of freshwater lakes is an important cause of global water pollution. In this study, the composition and biogeographic distribution of both abundant and rare sedimentary bacterial taxa and their relationship with nutrients were assessed in Erhai Lake, a subtropical plateau lake. Proteobacteria (48.3%) and Nitrospirae (11.7%) dominated the composition of abundant taxa, while the rare taxa were dominated by Proteobacteria (25.8%) and Chloroflexi (14.1%). The abundant bacterial taxa had strong energy metabolism, whereas the rare bacterial taxa had strong xenobiotics biodegradation and metabolism. These results indicated different compositions and functions existed between abundant and rare taxa. Total nitrogen (TN) was the most influential factor shaping the biogeographic patterns of both abundant and rare taxa. Phosphorus was not the deterministic factor, although nitrogen and phosphorus were the main contributors to eutrophication. Total organic carbon and pH also contributed to the biogeographic patterns of both abundant and rare taxa. In the eutrophic plateau lake sediments, abundant taxa, rather than rare taxa, played a dominant role in maintaining the community structure and ecological function of the bacterial community. The TN gradient was an important factor that affected the biogeographic distribution and assembly processes of abundant taxa. This study sheds light on the role of TN in shaping the biogeographic distribution and assembly processes of abundant taxa in eutrophic lakes.

Changes in microbial community diversity, composition, and functions upon nitrate and Cr(VI) contaminated groundwater

With the increasing occurrences of nitrate and Cr(VI) pollution globally, microbially driven pollutant reduction and its interaction effects were of growing interest. Despite the increasing number of experimental reports on the simultaneous reduction of nitrate and Cr(VI), a broad picture of the keystone species and metabolic differences in this process remained elusive. This study explored the changing of microorganisms with the introduction of Cr(VI)/NO₃^- through analyzing 242 samples from the NCBI database. The correlation between microbial abundance and environmental factors showed that, the types of energy substances and pollutants species in the environment had an impact on the diversity of microorganisms and community structure. The genus of Zoogloea, Candidatus Accumulibacter, and Candidatus Kapabacteria sp. 59-99 had the ability of denitrification, while genus of Alcaligenes, Kerstersia, Petrimonas, and Leucobacter showed effectively Cr(VI) resistance and reducing ability. Azoarcus, Pseudomonas, and Thauera were recognized as important candidates in the simultaneous reduction of nitrate and Cr(VI). Metagenomic predictions of these microorganisms using PICRUSt2 further highlighted the enrichment of Cr(VI)and nitrate reduction-related genes (such as chrA and norC). Special attention should therefore be paid to these bacteria in subsequent studies to evaluate their performance and mechanisms involved in simultaneous denitrification and chromium removal. The microbial co-occurrence network analysis conducted on this basis emphasized a strong association between community collaboration and pollution removal. Collectively, either site surveys or laboratory experiments, subsequent studies should focus on these microbial populations and the interspecific collaborations as they strongly influence the occurrence of simultaneous nitrate and Cr(VI) reduction.

Responses of the macrobenthic community to the Dalian Bay oil spill based on co-occurrence patterns and interaction networks

On July 16, 2010, a pipeline explosion spilled 1500 tons of crude oil into the Port of Dalian, China. To identify taxa responses to the spill, we exploited seven years of monitoring data to examine the co-occurrence of taxon pairs and the variation of the macrobenthic community. Non-parametric correlation analysis was used to construct interaction networks of relationships between oil spill contaminants and macrobenthic taxa. We observed that the impacted macrobenthic community not restored before 2016. The tolerance/sensitivity of taxa was inconsistent with the studies of oil impacts in other locations. We suggest revision of the ecological group classification of Sabellidae, Lumbrineridae, Terebellidae, Sternaspidae, and Spionidae. The variation in the frequency of coexistence indicates the potential impact of oil spill pollution on resource occupation. The interaction network involving macrobenthic families and stressors associated with the oil spill highlights how different macrobenthic families respond to different combinations of stressors.

Groundwater contaminated with short-chain chlorinated paraffins and microbial responses

The vertical migrations of toxic and persistent short-chain chlorinated paraffins (SCCPs) in soils as well as the microbial responses have been reported, however, there is a paucity of data on the resulting groundwater contamination. Here, we determined the concentration and congener profile of SCCPs in the groundwater beneath a production plant of chlorinated paraffins (CPs) and characterized the microbial community to explore their responses to SCCPs. Results showed that SCCPs ranged from not detected to 70.3 μg/L, with C₁₃-CPs (11.2-65.8%) and Cl₇-CPs (27.2-50.6%), in mass ratio, as the dominant groups. Similar to the distribution pattern in soils, SCCPs in groundwater were distributed in hotspot pattern. CP synthesis was the source of SCCPs in groundwater and the entire contamination plume significantly migrated downgradient, while there was an apparent hysteresis of C₁₃-CP migration. Groundwater microbial community was likely shaped by both hydrogeological condition (pH and depth) and SCCPs. Specifically, the microbial community responded to the contamination by forming a co-occurrence network with "small world" feature, where Desulfobacca, Desulfomonile, Ferritrophicum, Methylomonas, Syntrophobacter, Syntrophorhabdus, Syntrophus, and Thermoanaerobaculum were the keystone taxa. Furthermore, the interrelations between bacterial taxa and SCCPs indicated that the microbial community might cooperate to achieve the dechlorination and mineralization of SCCPs through either anaerobic organohalide respiration mainly functioned by the keystone taxa, or cometabolic degradation processes functioned by Aquabacterium and Hydrogenophaga. Results of this study would provide a better understanding of the environmental behavior and ecological effects of SCCPs in groundwater systems.

Stochastic processes drive bacterial and fungal community assembly in sustainable intensive agricultural soils of Shanghai, China

Sustainable intensive cropping systems have been implemented for three decades in suburban agricultural districts of Shanghai, China. These human-managed soils have been developed from paleosol or alluvial soils across different regions. However, little is known about the geographical distribution patterns of microbes and microbial community assembly in the sustainable intensive soils after decades of anthropogenic disturbances. Here, we investigated the impact of local geochemical properties and geographic distance on stochastic/deterministic microbial community assembly processes using high-throughput sequencing and phylogenetic null modeling analysis. Our results showed that soil pH was the most important environmental factor determining bacterial and fungal community structure. Importantly, only soil organic matter was positively correlated with fungal α-diversity, suggesting the efficient use of carbon substrates in sustainable agricultural systems, compensating for the lack of chemical fertilization and reduced tillage in these systems. Both bacterial and fungal communities had robust distance-decay patterns, but the rate of turnover of bacterial taxa was faster than that of fungi. Variation in bacterial and fungal communities was mostly attributed to the simultaneous effects of environmental variables and spatial factors. We also mapped the spatial distributions of the dominant bacterial and fungal taxa across the sustainable agricultural fields, making it possible to forecast the responses of agricultural ecosystems to anthropogenic disturbance. Based on the patterns of the β-nearest taxon index, this study demonstrated that stochastic processes shaped substantial bacterial and fungal community variation in sustainable intensive agricultural soils of the Shanghai suburbs. This variation may be attributed to the increasing microbial dispersal caused by hydrological connectivity in the agricultural fields or the release from environmental stress and weakened environmental filtering across the suitable pH range preferable for most soil microbes. These results unveil assembly mechanisms of soil microbial community after several decades of sustainable intensive management, and contribute to understand the role of microbes in ecosystems in establishing a functional equilibrium which may enable sustainability to be preserved.

Potential effects of Rhodococcus qingshengii strain djl-6 on the bioremediation of carbendazim-contaminated soil and the assembly of its microbiome

As a widely used fungicide, the environmental fate of carbendazim and its residues in agricultural products have caused great concern. However, its effects on soil microbial communities are largely unknown. Herein, we used high-throughput sequencing to reveal the effects of high and low dose of carbendazim and its degrading strain, Rhodococcus qingshengii strain djl-6, on the composition, diversity, and interrelationship of soil bacterial and fungal communities in short- and medium-term under laboratory conditions. The results showed that carbendazim exhibited an increased negative impact on bacterial communities and reduced the proportion of dominant fungal phylum Ascomycota during a 14-day incubation period. Only the impacts of low-dose carbendazim (2 mg·kg^-1 dry soil) on fungal community were weakened. Network analysis showed that carbendazim increased the connectivity and modularity of microbial co-occurrence networks. Strain djl-6 exhibited good potential for bioremediation of carbendazim-contaminated soils. Moreover, it driven the assembly of potential carbendazim-degrading consortia from indigenous microbial communities; and members of the genera Arthrobacter, Bacillus, Brevundimonas, Lysinibacillus, Massilia, Mycobacterium, Paenibacillus, and Pseudarthrobacter might be participated in the degradation of carbendazim. Taken together, our study provides a relatively comprehensive understanding of the effects of carbendazim and its degrading strain djl-6 on soil microbial communities.

Community assembly mechanisms and co-occurrence patterns of nitrite-oxidizing bacteria communities in saline soils

Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification by oxidizing nitrite to nitrate, which is a key process in the biogeochemical nitrogen cycling. However, little is known about the co-occurrence patterns and assembly processes of NOB communities in agricultural soils with different salinities. Here, we explored the effects of salinity on Nitrobacter and Nitrospira community using high-throughput sequencing and multivariate statistical analyses. Our results showed that high salinity significantly inhibited the nitrite oxidation rates and decreased the abundance of Nitrobacter and Nitrospira. Extreme salty conditions significantly altered the diversity and composition of Nitrospira community but had little effect on Nitrobacter community. Nitrobacter network in high salinity soils was more closely connected while the connectivity of Nitrospira network became weak. Nitrobacter and Nitrospira community exhibited distinct assembly processes at different salinity levels. Stochastic processes were dominant in the Nitrobacter community assembly in both low and high salinity soils. Interestingly, the assembly of Nitrospira community was governed by stochastic and deterministic processes in low and high salinity soils, respectively. To our knowledge, our study provides the first description of the co-occurrence patterns and assembly processes of NOB communities in agricultural soils with different salinities. These results can help us understand the NOB ecological roles and improve the nitrite oxidation activity in a high salinity environment.

The call for regional design code from the regional discrepancy of microbial communities in activated sludge

Discerning the differences in activated sludge (AS) microbial community due to geographic location and environmental and operational factors is of great significance for precise design and maintenance of wastewater treatment plants (WWTPs). Hence, in this study, 150 AS samples collected from WWTPs in South China and North China were analyzed by 16 S rRNA gene sequencing. In general, AS microbial community in North China had lower diversity, higher proportions of stochastic assembly (35.7% v.s. 15.8%) and more network keystone species (19 v.s. 5) compared with southern AS community. Conductivity and SRT had significant effects on AS community in both regions. Latitude, annual mean temperature, and influent BOD, COD, and ammonia influenced South China community significantly, while pH and influent total phosphorus affected North China community. To achieve stable performance, southern WWTPs should carefully monitor fluctuations in wastewater characteristics, while northern WWTPs should monitor AS communities for shifts in the dominant taxa from immigrant strains brought in through the influent. Additionally, WWTPs in North China should be aware of the need to proactively control sludge bulking because of the high abundance and occurrence of Haliscomenobacter in these AS communities. MAIN FINDING: The call for regional design based on the regional discrepancy of microbial communities in activated sludge is uncovered and according suggestions were given.

Long-term agricultural contamination shaped diversity response of sediment microbiome

The pollution caused by agricultural production poses a threat to the ecological integrity of river ecosystems, altering the structure and function of river ecosystems. Differences in microbial community structure provide useful information about the impact of agricultural pollution on the biological integrity of ecosystems, but generally convey little information regarding ecosystem functions. In this study, using Illumina MiSeq sequencing technology based on the 16S rRNA gene, river sediment samples associated with four different types of agricultural pollution were comprehensively analyzed. The results show that the total organic carbon (TOC) content was highest at the YZS site (animal husbandry sewage) among the assayed sites, but the species richness and uniformity were lowest at this site, which may have been caused by the high nutrient source of the sewage. Furthermore, in the three YZS samples affected by the long-term discharge of aquaculture tail-water, the unique genus Dechloromonas and the genus Candidatus-Competitor were observed, which are strongly correlated with phosphorus conversion. The formation of network modules may correspond to the coexistence of functional bacteria accustomed to multiple niche combinations under different agricultural pollution conditions in river sediments. According to the PICRUSt functional prediction, the bacterial community in the agricultural polluted river sediment primarily harbored 46 subfunctions, exhibiting richness of functions. Overall, our results provide a more comprehensive understanding of the structure and ecological processes associated with the aggregation of bacterial communities, which is beneficial for the management of river environments.

Response of protist community dynamics and co-occurrence patterns to the construction of artificial reefs: A case study in Daya Bay, China

Artificial reefs (ARs) are widely used for biodiversity conservation and coastal habitat restoration. Although protists play an important ecological role in marine ecosystems, the response of the protist community to ARs is still poorly understood. In the current study, an Illumina sequencing analysis of 18S rDNA was performed, and the diversity, community structure, and co-occurrence networks of protists in the ARs and open sea area (OW) in Daya Bay were described. The results indicated that significant seasonal differences occur in the seawater protists between the surface and bottom of the ARs and OW. However, the protists in the ARs and OW had different seasonal variations. The ARs always affected the alpha diversity of marine protists in different seasons, while the surface and bottom OW sites had different seasonal effects. The ARs sites had different effects on the community composition of the surface and bottom seawater in different seasons relative to the OW sites. The linear discriminant analysis (LDA) effect size (LEfSe) method showed that 85 biomarkers mainly belonging to 11 taxa, including Bacillariophyta, Chlorophyta, and Dinophyceae, were affected by the ARs (P < 0.05, LDA > 2.0). The ARs played an important role in the seasonal changes in the protist community composition and had different effects on the dominant species of protists in the surface and bottom seawater. A redundancy analysis (RDA) significance test showed that the structure of the protist community in Daya Bay was mainly affected by environmental factors, such as seawater temperature, salinity and dissolved oxygen. Compared with the OW group, the surface and bottom layers of the ARs had more complex protist interactions or more niches. The ARs increased the degree of spatial heterogeneity, which may lead to significant niche differentiation, indicating that ARs as habitat factors affect the complexity and stability of the symbiotic network of protists. The results could provide basic data on the response of the protist community to the ARs in Daya Bay and a reference for assessments of the impact of ARs on the ecological environment.

Elevation rather than season determines the assembly and co-occurrence patterns of soil bacterial communities in forest ecosystems of Mount Gongga

Seasonal dynamics of soil microbial communities may influence ecosystem functions and services. However, few observations have been conducted on the dynamics of a bacterial community assembly across seasons in different elevations in mountain forest ecosystems. In this study, the diversity, compositions, community assembly processes, and co-occurrence interactions of soil bacterial communities were investigated using Illumina sequencing of 16S rRNA genes across different seasons during two consecutive years (2016 and 2017) at two elevational sites in Mount Gongga, China. These two sites included an evergreen broad-leaved forest (EBF, 2100 m a.s.l.) and a dark coniferous forest (DCF, 3000 m a.s.l.). The results showed that bacterial diversity and structure varied considerably between the two elevational sites with only limited seasonal variations. Interannuality had a significant effect on the diversity and structure of soil bacterial communities. The bacterial alpha diversity was significantly higher at site EBF(e.g., OTUs richness, 2207 ± 276) than at site DCF(e.g., OTUs richness, 1826 ± 315). Soil pH, temperature, elevation, and water content were identified as important factors shaping soil bacterial communities in the mountain forests. Bacterial community assembly was primarily governed by deterministic processes regardless of elevation and season. Deterministic processes were stronger at site DCF than at EBF. The soil bacterial community at site EBF harbored a more complex and connected network with less resistance to environmental changes. Overall, this study showed that seasonal dynamics of bacterial communities were much weaker than those along elevations, implying that a single-season survey on a bacterial community along an elevational gradient can represent overall changes in the bacterial community. KEY POINTS: • Seasonal dynamics of soil bacterial communities were studied in Mount Gongga. • The bacterial community was mainly affected by elevation rather than season. • Deterministic processes dominated bacterial community assembly. • The bacterial network was more complex but less stable at EBF than at DCF.

River bacterial community structure and co-occurrence patterns under the influence of different domestic sewage types

Bacterial communities play a critical role in food webs and the biogeochemical cycles of fundamental elements. However, there remains a substantial gap in our knowledge of the anthropogenic impacts on bacterial co-occurrence patterns and ecosystem functions. In this study, we used Illumina high-throughput sequencing to characterize and compare the diversity, composition, co-occurrence patterns, and functional changes in bacterial communities in the Qingliu River under the influence of different types of domestic sewage. Twelve samples had similar dominant phyla, mainly Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes, differing only in the proportions of the microorganisms. However, there was a large difference at the genus level, for example, the relative abundance of the genus Dechloromonas in the school sewage water samples (XXW) was much higher than that in the other samples, the genus Chryseobacterium was the dominant bacteria in the residential sewage water samples (JMW), and there were significant differences between the different samples (P < 0.01). This may indicate that external pollution and environmental induction deeply affect the bacterial community assembly in rivers. Network analysis showed that the river bacterial co-occurrence network has a modular structure (divided into 6 modules), and that the microbial taxonomic units from the same module were involved in the carbon and nitrogen cycle (e.g., the CL500-29 marine group and the genus Pseudomonas) and degradation of organic pollutants and toxic compounds (e.g., the genera Massilia and Exiguobacterium). Functional predictions indicate that the function of ABC transporter was highest in the hospital sewage water samples (YYW), while two-component system was more abundant in the XXW samples. In summary, our research provides a new perspective of community assembly in rivers under the influence of human activity.

Distributions of chlorinated paraffins and the effects on soil microbial community structure in a production plant brownfield site

The distributions of chlorinated paraffins (CPs) in soils and their ecological effects attract much attention, while site-scale data are still scarce. In this study, a comprehensive investigation was performed to understand the CP distributions at a CP production plant brownfield site, as well as their effects on soil microbial community. Short-, medium- and long-chain CPs (SCCPs, MCCPs, LCCPs) were detected in most samples with total contents ranging ND-5,090, ND-6,670, and ND-1450 ng g^-1 (dw), respectively. A CP-hotspot was observed 10 m beneath the synthesis workshop, indicating the downward migration of CPs. The consistence of soil SCCP congener profiles with commercial product CP-52 suggested the leakage of CP products as the contamination source. Besides CPs, petroleum hydrocarbons (PHC) contamination also occurred beneath the synthesis workshop. Soil microbial community composition and diversity were significantly influenced by SCCPs (p < 0.05) despite their lower contents compared to other concerned contaminants. Microbial network analysis indicated nonrandom co-occurrence patterns, with Acinetobacter, Brevibacterium, Corynebacterium, Microbacterium, Stenotrophomonas, and Variibacter as the keystone genera. Genera from the same module showed significant ecological links (p < 0.05) and were involved in the degradation of PHCs and chlorinated organic contaminants. This study provides the first phylogenetic look at the microbial communities in CP contaminated soils, indicating that the long-term exposure to CPs and PHCs may lead to microbial group assemblages with the potential for degradation.

Earth microbial co-occurrence network reveals interconnection pattern across microbiomes

BACKGROUND

Microbial interactions shape the structure and function of microbial communities; microbial co-occurrence networks in specific environments have been widely developed to explore these complex systems, but their interconnection pattern across microbiomes in various environments at the global scale remains unexplored. Here, we have inferred an Earth microbial co-occurrence network from a communal catalog with 23,595 samples and 12,646 exact sequence variants from 14 environments in the Earth Microbiome Project dataset.

RESULTS

This non-random scale-free Earth microbial co-occurrence network consisted of 8 taxonomy distinct modules linked with different environments, which featured environment specific microbial co-occurrence relationships. Different topological features of subnetworks inferred from datasets trimmed into uniform size indicate distinct co-occurrence patterns in the microbiomes of various environments. The high number of specialist edges highlights that environmental specific co-occurrence relationships are essential features across microbiomes. The microbiomes of various environments were clustered into two groups, which were mainly bridged by the microbiomes of plant and animal surface. Acidobacteria Gp2 and Nisaea were identified as hubs in most of subnetworks. Negative edges proportions ranged from 1.9% in the soil subnetwork to 48.9% the non-saline surface subnetwork, suggesting various environments experience distinct intensities of competition or niche differentiation. Video abstract CONCLUSION: This investigation highlights the interconnection patterns across microbiomes in various environments and emphasizes the importance of understanding co-occurrence feature of microbiomes from a network perspective.

Emergence and spread patterns of antibiotic resistance genes during two different aerobic granular sludge cultivation processes

The prevalence and accumulation of antibiotic resistance genes (ARGs) were frequently detected in biological wastewater treatment processes, which might cause potential health crisis to human. In present study, the fates of ARGs during two different aerobic granular sludge (AGS) cultivation processes were investigated. The results showed that traditional AGS (T-AGS) cultivation process and enhanced AGS (E-AGS) cultivation process had significant differences (P < 0.005) in ARGs shift patterns. E-AGS process had higher average relative abundance (0.280 ± 0.079) of ARGs than T-AGS process (0.130 ± 0.041), while the intensity of ARGs enrichment during E-AGS (1.52-5.29 fold) was lower than T-AGS (3.79-75.31 fold) process. TnpA and intI1 as two different types of mobile genetic elements (MGEs) carrying ARGs, were observed to contribute significantly to the horizontal gene transfer (HGT) during T-AGS (r = 0.902, P < 0.050) and E-AGS (r = 0.823, P < 0.001) processes, respectively. Higher HGT level took place and more possible potential hosts (25 hosts) harboring ARGs were detected during E-AGS process comparing with T-AGS process (17 hosts). Meanwhile, over large AGS might increase the propagation of several antibiotic deactivation ARGs, so it was not advised. Overall, whether during T-AGS or during E-AGS process which was applied in a pilot-scale sequencing batch reactor treating municipal wastewater, the accumulation and spread of ARGs were inevitable. It should be valued that some suitable pre-treatments of seed sludge should be executed, meanwhile, advanced treatment for removing of ARGs in AGS should be conducted to maintain the relative abundances of ARGs at relatively low level.

Co-occurrence patterns of bacteria within microbiome of Moscow subway

Microbial ecosystems of the built environments have become key mediators of health as people worldwide tend to spend large amount of time indoors. Underexposure to microbes at an early age is linked to increased risks of allergic and autoimmune diseases. Transportation systems are of particular interest, as they are globally the largest space for interactions between city-dwellers. Here we performed the first pilot study of the Moscow subway microbiome by analyzing swabs collected from 5 types of surfaces at 4 stations using high-throughput 16S rRNA gene sequencing. The study was conducted as a part of The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) project. The most abundant microbial taxa comprising the subway microbiome originated from soil and human skin. Microbiome diversity was positively correlated with passenger traffic. No substantial evidence of major human pathogens presence was found. Co-occurrence analysis revealed clusters of microbial genera including combinations of microbes likely originating from different niches. The clusters as well as the most abundant microbes were similar to ones obtained for the published data on New-York City subway microbiome. Our results suggest that people are the main source and driving force of diversity in subway-associated microbiome. The data form a basis for a wider survey of Moscow subway microbiome to explore its longitudinal dynamics by analyzing an extended set of sample types and stations. Complementation of methods with viability testing, "shotgun" metagenomics, sequencing of bacterial isolates and culturomics will provide insights for public health, biosafety, microbial ecology and urban design.

Spatial-Temporal Variation of Bacterial Communities in Sediments in Lake Chaohu, a Large, Shallow Eutrophic Lake in China

Sediment bacterial communities are critical for the circulation of nutrients in lake ecosystems. However, the bacterial community function and co-occurrence models of lakes have not been studied in depth. In this study, we observed significant seasonal changes and non-significant spatial changes in the beta diversity and community structure of sediment bacteria in Lake Chaohu. Through linear discriminant analysis effect size (LEfSe), we observed that certain taxa (from phylum to genus) have consistent enrichment between seasons. The sudden appearance of a Firmicutes population in spring samples from the Zhaohe River, an estuary of Lake Chaohu, and the dominance of Firmicutes populations in other regions suggested that exogenous pollution and environmental induction strongly impacted the assembly of bacterial communities in the sediments. Several taxa that serve as intermediate centers in Co-occurrence network analysis (i.e., Pedosphaeraceae, Phycisphaeraceae, Anaerolineaceae, and Geobacteraceae) may play an important role in sediments. Furthermore, compared with previous studies of plants and animals, the results of our study suggest that various organisms, including microorganisms, are resistant to environmental changes and/or exogenous invasions, allowing them to maintain their community structure.

Distribution Patterns of Microbial Community Structure Along a 7000-Mile Latitudinal Transect from the Mediterranean Sea Across the Atlantic Ocean to the Brazilian Coastal Sea

A central goal in marine microecology is to understand the ecological factors shaping spatiotemporal microbial patterns and the underlying processes. We hypothesized that abiotic and/or biotic interactions are probably more important for explaining the distribution patterns of marine bacterioplankton than environmental filtering. In this study, surface seawater samples were collected about 7000 miles from the Mediterranean Sea, transecting the North Atlantic Ocean, to the Brazilian marginal sea. In bacterial biosphere, SAR11, SAR86, Rhodobacteraceae, and Rhodospiriaceae were predominant in the Mediterranean Sea; Prochlorococcus was more frequent in Atlantic Ocean; whereas in the Brazilian coastal sea, the main bacterial members were Synechococcus and SAR11. With respect to archaea, Euryarchaeota were predominant in the Atlantic Ocean and Thaumarchaeota in the Mediterranean Sea. With respect to the eukaryotes, Syndiniales, Spumellaria, Cryomonadida, and Chlorodendrales were predominant in the open ocean, while diatoms and microzooplankton were dominant in the coastal sea. Distinct clusters of prokaryotes and eukaryotes displayed clear spatial heterogeneity. Among the environmental parameters measured, temperature and salinity were key factors controlling bacterial and archaeal community structure, respectively, whereas N/P/Si contributed to eukaryotic variation. The relative contribution of environmental parameters to the microbial distribution pattern was 45.2%. Interaction analysis showed that Gammaproteobacteria, Alphaproteobacteria, and Flavobacteriia were the keystone taxa within the positive-correlation network, while Thermoplasmata was the main contributor in the negative-correlation network. Our study demonstrated that microbial communities are co-governed by environmental filtering and biotic interactions, which are the main deterministic driving factors modulating the spatiotemporal patterns of marine plankton synergistically at the regional or global levels.

The Diversity and Co-occurrence Patterns of N₂-Fixing Communities in a CO₂-Enriched Grassland Ecosystem

Diazotrophs are the major organismal group responsible for atmospheric nitrogen (N2) fixation in natural ecosystems. The extensive diversity and structure of N2-fixing communities in grassland ecosystems and their responses to increasing atmospheric CO2 remain to be further explored. Through pyrosequencing of nifH gene amplicons and extraction of nifH genes from shotgun metagenomes, coupled with co-occurrence ecological network analysis approaches, we comprehensively analyzed the diazotrophic community in a grassland ecosystem exposed to elevated CO2 (eCO2) for 12 years. Long-term eCO2 increased the abundance of nifH genes but did not change the overall nifH diversity and diazotrophic community structure. Taxonomic and phylogenetic analysis of amplified nifH sequences suggested a high diversity of nifH genes in the soil ecosystem, the majority belonging to nifH clusters I and II. Co-occurrence ecological network analysis identified different co-occurrence patterns for different groups of diazotrophs, such as Azospirillum/Actinobacteria, Mesorhizobium/Conexibacter, and Bradyrhizobium/Acidobacteria. This indicated a potential attraction of non-N2-fixers by diazotrophs in the soil ecosystem. Interestingly, more complex co-occurrence patterns were found for free-living diazotrophs than commonly known symbiotic diazotrophs, which is consistent with the physical isolation nature of symbiotic diazotrophs from the environment by root nodules. The study provides novel insights into our understanding of the microbial ecology of soil diazotrophs in natural ecosystems.

Missing checkerboards? An absence of competitive signal in Alnus-associated ectomycorrhizal fungal communities

A number of recent studies suggest that interspecific competition plays a key role in determining the structure of ectomycorrhizal (ECM) fungal communities. Despite this growing consensus, there has been limited study of ECM fungal community dynamics in abiotically stressful environments, which are often dominated by positive rather than antagonistic interactions. In this study, we examined the ECM fungal communities associated with the host genus Alnus, which live in soils high in both nitrate and acidity. The nature of ECM fungal species interactions (i.e., antagonistic, neutral, or positive) was assessed using taxon co-occurrence and DNA sequence abundance correlational analyses. ECM fungal communities were sampled from root tips or mesh in-growth bags in three monodominant A. rubra plots at a site in Oregon, USA and identified using Illumina-based amplification of the ITS1 gene region. We found a total of 175 ECM fungal taxa; 16 of which were closely related to known Alnus-associated ECM fungi. Contrary to previous studies of ECM fungal communities, taxon co-occurrence analyses on both the total and Alnus-associated ECM datasets indicated that the ECM fungal communities in this system were not structured by interspecific competition. Instead, the co-occurrence patterns were consistent with either random assembly or significant positive interactions. Pair-wise correlational analyses were also more consistent with neutral or positive interactions. Taken together, our results suggest that interspecific competition does not appear to determine the structure of all ECM fungal communities and that abiotic conditions may be important in determining the specific type of interaction occurring among ECM fungi.