Bacterial Community Assembly Processes Research Articles

Spatial distribution and assembly processes of bacterial communities in riverine and coastal ecosystems of a rapidly urbanizing megacity in China

Rapid urbanization has precipitated significant anthropogenic pollution (nutrients and pathogens) in urban rivers and their receiving systems, which consequentially disrupted the compositions and assembly of bacterial community within these ecosystems. However, there remains scarce information regarding the composition and assembly of both planktonic and benthic bacterial communities as well as pathogen distribution in such environments. In this study, full-length 16S rRNA gene sequencing was conducted to investigate the bacterial community composition, interactions, and assembly processes as well as the distribution of potential pathogens along a riverine-coastal continuum in Shenzhen megacity, China. The results indicated that both riverine and coastal bacterial communities were predominantly composed of Gammaproteobacteria (24.8 ± 12.6 %), Alphaproteobacteria (16.1 ± 9.8 %), and Bacteroidota (14.3 ± 8.6 %), while sedimentary bacterial communities exhibited significantly higher diversity compared to their planktonic counterparts. Bacterial community patterns exhibited significant divergences across different habitats, and a significant distance-decay relationship of bacterial community similarity was particularly observed within the urban river ecosystem. Moreover, the urban river ecosystem displayed a more complex bacterial co-occurrence network than the coastal ecosystem, and a low ratio of negative:positive cohesion suggested the inherent instability of these networks. Homogeneous selection and dispersal limitation emerged as the predominant influences on planktonic and sedimentary bacterial communities, respectively. Pathogenic genera such as Vibrio, Bacteroides, and Acinetobacter, known for their roles in foodborne diseases or wound infection, were also identified. Collectively, these findings provided critical insights into bacterial community dynamics and their implications for ecosystem management and pathogen risk control in riverine and coastal environments impacted by rapid urbanization.

Parent material influences soil properties to shape bacterial community assembly processes, diversity, and enzyme-related functions

Soil parent material is the second most influential factor in pedogenesis, influencing soil properties and microbial communities. Different assembly processes shape diverse functional microbial communities. The question remains unresolved regarding how these ecological assembly processes affect microbial communities and soil functionality within soils on different parent materials. We collected soil samples developed from typical parent materials, including basalt, granite, metamorphic rock, and marine sediments across soil profiles at depths of 0–20, 20–40, 40–80, and 80–100 cm, within rubber plantations on Hainan Island, China. We determined bacterial community characteristics, community assembly processes, and soil enzyme-related functions using 16S rRNA high-throughput sequencing and enzyme activity analyses. We found homogeneous selection, dispersal limitation, and drift processes were the dominant drivers of bacterial community assembly across soils on different parent materials. In soils on basalt, lower pH and higher moisture triggered a homogeneous selection-dominated assembly process, leading to a less diverse community but otherwise higher carbon and nitrogen cycling enzyme activities. As deterministic process decreased, bacterial community diversity increased with stochastic process. In soils on marine sediments, lower water, carbon, and nutrient content limited the dispersal of bacterial communities, resulting in higher community diversity and an increased capacity to utilize relative recalcitrant substrates by releasing more oxidases. The r-strategy Bacteroidetes and genera Sphingomonas, Bacillus, Vibrionimonas, Ochrobactrum positively correlated with enzyme-related function, whereas k-strategy Acidobacteria, Verrucomicrobia and genera Acidothermus, Burkholderia-Caballeronia-Paraburkholderia, HSB OF53-F07 showed negative correlations. Our study suggests that parent material could influence bacterial community assembly processes, diversity, and soil enzyme-related functions via soil properties.

Deciphering the role of biotic factors in community assembly and diversity patterns of soil bacterial communities under different land use

Environmental heterogeneities in climate and soil properties have been recognized as key factors structuring the bacterial community at large scale. Although recent evidence has demonstrated the importance of local biotic interactions in driving soil bacterial communities, it is remains unclear how biotic filtering affects bacterial diversity patterns at large scale. Here, we explored the effect of biotic factors on bacterial community assembly and diversity pattern in agricultural and natural ecosystems based on a continental-scale investigation across a 3689 km latitudinal gradient in Eastern China. Despite of the distinct diversity patterns of soil bacterial communities along latitudes in different ecosystems, biotic factors (the fungal and protist communities) were consistently identified as the most important predictor of the latitudinal variations in the bacterial communities, even when considering the influence from climate and soil variables. The bacterial community assembly processes were dominated by homogeneous selection and were primarily affected by soil pH and protist consumers in upland and forest soils but by fungi and protist phototrophs in paddy soils. The bipartite networks between bacteria, fungi and protists provide further evidence that network complexity and specific interdomain interactions may influence the latitudinal distribution of bacteria, in land use-dependent patterns. Our study provides a novel insight into the critical role of biotic factor in shaping geographic patterns of soil bacterial communities, with important implications for maintaining soil large-scale biodiversity and functions.

Stochastic and deterministic assembly processes of bacterial communities in different soil aggregates

Soil bacterial community assembly determined by both the niche-based deterministic and the stochastic process. However, at aggregate scale, the contribution and limitation of those theories in soil bacterial community assembly process still unknown. In this study, different aggregate fractions with a water-controllable unit were performed to build a simple system, aiming to (i) exhibit a contrasting bacterial community assembly pattern of aggregate fractions after incubation under different water content, (ii) quantify the variations of bacterial community during incubation caused by niches or deterministic factors of physic-chemical characteristics, and (iii) assess the pore water driven immigration rates of neutral or stochastic processes caused by different aggregate fractions on bacterial community assembly by neutral community model (NCM). We found a significantly time-decay of bacteria community of different soil aggregate fractions during the incubation period. Despite of the decrease of the total OTU amounts, the proportion of the unique OTUs in the aggregates of <0.25 mm and shared OTUs in three soil aggregate fractions increased under both saturated and unsaturated conditions. Microbial communities in aggregates of <0.25 mm were more distinctive enriched the core microbiota of Firmicutes and Proteobacteria than other aggregates, which might relate to the higher availability N and pH value. Under water saturated situation, bacterial migration rate of 0.25–1 mm at the early-stage was higher than others indicated the ineligible role of water-driven bacterial dispersal on bacterial community assembly process. Those results revealed the deterministic and stochastic mechanism of soil bacterial community assembly at aggregate scale, which helps to unravel the mysterious soil habitat.

Influence of sedimentary deposition on the microbial assembly process in Arctic Holocene marine sediments.

The sea-level rise during the Holocene (11-0 ky BP) and its resulting sedimentation and biogeochemical processes may control microbial life in Arctic sediments. To gain further insight into this interaction, we investigated a sediment core (up to 10.7 m below the seafloor) from the Chuckchi Shelf of the western Arctic Ocean using metabarcoding-based sequencing and qPCR to characterize archaeal and bacterial 16S rRNA gene composition and abundance, respectively. We found that Arctic Holocene sediments harbor local microbial communities, reflecting geochemical and paleoclimate separations. The composition of bacterial communities was more diverse than that of archaeal communities, and specifically distinct at the boundary layer of the sulfate-methane transition zone. Enriched cyanobacterial sequences in the Arctic middle Holocene (8-7 ky BP) methanogenic sediments remarkably suggest past cyanobacterial blooms. Bacterial communities were phylogenetically influenced by interactions between dispersal limitation and environmental selection governing community assembly under past oceanographic changes. The relative influence of stochastic and deterministic processes on the bacterial assemblage was primarily determined by dispersal limitation. We have summarized our findings in a conceptual model that revealed how changes in paleoclimate phases cause shifts in ecological succession and the assembly process. In this ecological model, dispersal limitation is an important driving force for progressive succession for bacterial community assembly processes on a geological timescale in the western Arctic Ocean. This enabled a better understanding of the ecological processes that drive the assembly of communities in Holocene sedimentary habitats affected by sea-level rise, such as in the shallow western Arctic shelves.

Mowing effects on soil bacterial community assembly processes in a semiarid grassland

Mowing effects on soil bacterial community assembly processes in a semiarid grassland

Changes in soil stoichiometry, soil organic carbon mineralization and bacterial community assembly processes across soil profiles

Soil organic carbon (SOC) mineralization is essential to biogeochemical recycling in terrestrial ecosystem. However, the microbial mechanisms underlying the nutrient-induced SOC mineralization remain uncertain. Here, we investigated how SOC mineralization was linked to microbial assembly processes as well as soil nutrient availability and stoichiometric ratio in a paddy rice ecosystem at four soil profile levels. Our results showed a sharp decrease in SOC mineralization from topsoil (112.61–146.34 mg CO2 kg−1 day−1) to subsoil (33.51–61.41 mg CO2 kg−1 day−1). High-throughput sequencing showed that both abundance and diversity of specialist microorganisms (Chao1: 1244.30–1341.35) significantly increased along the soil profile, while the generalist microorganisms (Chao1: 427.67–616.15; Shannon: 7.46–7.97) showed the opposite trend. Correspondingly, the proportion of deterministic processes that regulate specialist (9.64–21.59 %) and generalist microorganisms (21.17–53.53 %) increased and decreased from topsoil to subsoil, respectively. Linear regression modeling and partial least squares path modeling indicated that SOC mineralization was primarily controlled by the assembly processes of specialist microorganisms, which was significantly mediated by available soil C:N:P stoichiometry. This study highlighted the importance of soil stoichiometry-mediated bacterial community assembly processes in regulating SOC mineralization. Our results have an important implication for the integration of bacterial community assembly processes into the prediction of SOC dynamics.

Structure, variation and assembly processes of bacterial communities in different niches of tomato rhizosphere under periodic drought and nitrogen addition

Root-associated bacteria play a vital role in the growth and adaptation of host plants to drought stress. These bacteria can be classified as rhizoplane and rhizosphere bacteria based on their distance from the root surface. Tomato plants are often exposed to periodic droughts and nitrogen (N) addition throughout their life cycle, but the impact of these factors on the plant and root-associated bacteria is not well understood. To gain insight into this relationship, we conducted a study to monitor the effects of periodic droughts and N addition on tomato plants’ rhizoplane and rhizosphere bacteria. Drought and N addition had interactive effects in affecting plant and soil properties, which varied with the timing of drought. There were clear divergences in community traits such as alpha, beta diversity and network topological features between the two types of bacteria. The rhizoplane bacteria showed lower alpha diversity but higher beta diversity and were more sensitive to drought and N addition than the rhizosphere bacteria. Nitrogen addition could downsize the effects of drought on rhizoplane bacterial community compositions. The higher proximity to the root might induce a community to develop more cooperation between different members to cope with plant metabolites, as revealed by the more connected and modularized community network of the rhizoplane bacteria. Drought at the seedling stage had great legacy effects on plant and soil properties. It may enhance selection, cause the dominance of deterministic processes in the assembly of rhizoplane bacteria, and reduce their community network complexity. In conclusion, N addition could interact with drought in affecting tomato plants and their root-associated bacteria, depending on the timing of drought and the finer root niches. The higher sensitivity of rhizoplane bacteria to drought and N addition calls for more research due to their higher proximity and importance to plants in future environmental changes.

Spatial distribution and assembly processes of bacterial communities in northern Florida freshwater springs

Freshwater microorganisms are an essential component of the global biogeochemical cycle and a significant contributory factor in water quality. Unraveling the mechanisms controlling microbial community spatial distribution is crucial for the assessment of water quality and health of aquatic ecosystems. This research provided a comprehensive analysis of microbial communities in Florida freshwater springs. The 16S rRNA gene sequencing and bioinformatics analyses revealed the bacterial compositional heterogeneity as well as numerous unique ASVs and biomarkers in different springs. Statistical analysis showed both geographic distance and environmental variables contributed to regional bacterial community variation, while nitrate was the dominant environmental stressor that shaped the bacterial communities. The phylogenetic bin-based null model characterized both deterministic and stochastic factors contributing to community assembly in Florida springs, with the majority of bins dominated by ecological drift. Mapping of predicted pathways to the MetaCyc database revealed the inconsistency between microbial taxonomic and functional profiles, implying the functional redundancy pattern. Collectively, our work sheds insights into the microbial spatial distribution, community assembly, and function traits in one of the world's most productive aquifers. Therefore, this work provides a unique view of the health of Florida's artesian springs and offers new perspectives for freshwater quality assessment and sustainable management.

Seasonality and bacterial community assembly processes dominate prairie ecosystem service disruption during invasion

Invasive plants alter soil microbial communities and ecosystem services reducing the Earth's carrying capacity for humans. Many ecosystem services are underpinned by soil microbial communities, and these communities arise from assembly processes that are likely altered by invasion. We evaluated the hypothesis that invasive effects on grassland ecosystem services arise from changes in microbial community assembly processes caused by invasion. We sampled 515 plots at a native Rough Fescue prairie undergoing invasion by nine invasive species of which smooth brome (Bromus inermis) is a dominant member. Each week, for 26 weeks, we monitored invasion effects on vascular plant communities, ecosystem services, as well as bacterial and fungal community structures. Invasive effects on ecosystem services interacted with seasonal (plant green-up, peak biomass, and plant senescence) effects and consistently disrupted ecosystem service provision. Invasion increased heterogenous selection in fungal communities but otherwise had minor effects on assembly process. Only ∼20% of community composition could be ascribed to deterministic filters which hindered our ability to conclusively link invasion to assembly processes. Assembly processes explained changes in ecosystem services with bacterial assembly accounting for 2.5% of food, 4% of climate, 9% of conservation and 5.5% of fertility services. Fungal communities were less consistent in their effects on ecosystem services with only food (3%) and water (4%) services influenced by fungal assembly. After seasonality (27%), bacterial assembly processes (4%) accounted for the largest effect on ecosystem services, overshadowing invasion (2%) and fungal assembly (2%). At this 130-ha site, after seasonal effects, bacterial assembly processes had the largest effect on ecosystem services with plant invasion placing a distant third.

Grazing and reclamation-induced microbiome alterations drive organic carbon stability within soil aggregates in alpine steppes

Grazing and reclamation are the major modulators of soil organic carbon (SOC) stability in alpine steppes. However, our understanding of changes in SOC caused by grazing and reclamation at the aggregate scale is limited, and the mediating role of microorganisms remains unclear. Here, based on a long-term observation transect, we selected three land-use types: a long-term enclosed natural steppe (NS), a grazed steppe (GS), and a steppe reclaimed as cropland (CL). We investigated the impacts of grazing and reclamation on soil aggregate distributions, SOC fractions and the microbial community, and microbial contributions to SOC stability. Overall, GS and CL significantly decreased the proportion of >2 mm aggregates (by 32.25–33.72%), and enhanced SOC stability within different aggregate sizes, with the highest SOC stability observed in 0.25–2 mm and <0.25 mm sizes. GS significantly decreased bacterial diversity and increased the relative abundance of Gammaproteobacteria, while CL significantly increased microbial diversity and the relative abundance of Alphaproteobacteria. Importantly, GS enhanced the complexity of the bacterial OTUs networks in >2 mm and <0.25 mm aggregates. GS and CL caused changes in the assembly processes of bacterial communities, shifting from being mainly controlled by variable selection to being mainly controlled by homogenizing dispersal. However, there were only minor differences observed in the microbial community assembly within different aggregate sizes under the same treatment. Random forest models and correlation analysis revealed that the bacterial community, especially the network patterns and community assembly, was a key determinant of SOC stability in soil aggregates. In conclusion, we emphasize the important contribution of soil bacterial network patterns and community assembly to SOC stability in the context of human activities, providing information that may be useful for developing alpine steppe management strategies to enhance soil carbon sequestration.

Limited impacts of high doses of dietary copper on the gut bacterial metal resistome explain negligible co-selection of antibiotic resistance

High dietary intake of Cu has previously been linked to the selection of Cu resistance and co-selection of antibiotic resistance in specific gut bacteria. Based on a novel HT-qPCR metal resistance gene chip as combined with 16S rRNA gene amplicon sequencing and phenotypic resistance typing of Escherichia coli isolates, we here report the impacts of two contrasting Cu-based feed additives on the swine gut bacterial metal resistome and community assembly. DNA was extracted from fecal samples (n = 80) collected at day 26 and 116 of the experiment from 200 pigs allotted to five dietary treatments: negative control (NC) diet with 20 μg CuSO4 g−1 and four diets added 125 or 250 μg CuSO4 g−1 feed or 125 or 250 μg Cu2O g−1 feed to the NC diet. Dietary Cu supplementation reduced the relative abundance of Lactobacillus, but it had negligible impacts on bacterial community composition relative to the gut microbiome maturation effect (time). The relative importance of different bacterial community assembly processes was not markedly affected by the dietary Cu treatments, and differences in swine gut metal resistome composition could be explained primarily by differences in bacterial community composition rather than by dietary Cu treatments. High dietary Cu intake (250 μg Cu g−1) selected for phenotypic Cu resistance in E. coli isolates, but surprisingly it did not result in increased prevalence of the Cu resistance genes targeted by the HT-qPCR chip. In conclusion, the lacking impacts of dietary Cu on the gut bacterial metal resistome explain results from a previous study showing that even high therapeutic doses of dietary Cu did not cause co-selection of antibiotic resistance genes and mobile genetic elements known to harbor these genes.

Effects of biochar addition on aeolian soil microbial community assembly and structure

The effects of biochar on soil improvement have been widely confirmed, but its influence on soil microorganisms is still unclear. Elucidating the complex relationship and the community assembly processes of microorganisms under biochar addition is important to understand the ecological effects of this substance. We performed a one-time addition of biochar on aeolian soils and planted maize (Zea mays L.) continuously for 7 years. Afterwards, soil samples were collected, and the 16S/ITS rRNA gene sequencing technology was used to study changes in microbial community structure, network characteristics, and community assembly processes in the aeolian soils. We found that biochar addition significantly increased the maize yield and changed the soil microbial community composition (β-diversity), but had no significant effect on the microbial α-diversity. The addition of 31.5-126.0 Mg ha-1 of biochar led to a reduction of the rhizosphere bacterial network's edge number, average degree, and robustness, but had no significant effect on the fungal network properties. The bacterial community was controlled by deterministic processes, while fungi were mainly controlled by stochastic processes. The addition of 126.0 Mg ha-1 of biochar led to a transformation of the bacterial community's assembly processes from deterministic to stochastic. These results indicate that the stability of the rhizosphere bacterial community's complex network in aeolian soils diminishes under biochar addition, together changed the bacterial community's assembly processes. Fungi can instead effectively resist the environmental changes brought by biochar addition, and their network remains unchanged. These findings help clarify the effect of biochar addition on microbial interaction and assembly processes in aeolian soils characteristic of arid regions. KEY POINTS: • Biochar addition led to changes in the microbial community composition • Biochar addition reduced the network's stability of rhizosphere bacteria • Biochar addition changed the processes of the bacterial community assembly.

Plastisphere microbiome: Methodology, diversity, and functionality.

Broad topics of the plastisphere in various environments are reviewed, including its methodologies, diversity, functionality, and outlook.

Bacterial community assembly and antibiotic resistance genes in soils exposed to antibiotics at environmentally relevant concentrations.

Understanding how bacterial community assembly and antibiotic resistance genes (ARGs) respond to antibiotic exposure is essential to deciphering the ecological risk of anthropogenic antibiotic pollution in soils. In this study, three loam soils with different land management (unmanured golf course, dairy-manured pasture, and swine-manured cornfield) were spiked with a mixture of 11 antibiotics at the initial concentration of 100 and 1000 μg kg-1 for each antibiotic and incubated over 132 days, mimicking a scenario of pulse disturbance and recovery in soils, with unspiked soil samples as the control treatment. The Infer Community Assembly Mechanisms by Phylogenetic-bin-based null model (iCAMP) analysis demonstrated that drift and dispersal limitation contributed to 57%-65% and 16%-25%, and homogeneous selection 12%-16% of soil bacterial community assembly. Interestingly, antibiotic exposure to 1000 μg kg-1 level significantly increased the contribution of drift to community assembly, largely due to the positive response from Acidobacteria-6 in the golf course and pasture soilsand from Chthoniobacteraceae in the cornfield soil to the antibiotic exposure. However, ARG abundance and diversity in the three soils exhibited antibiotics-independent temporal fluctuations, but were associated with the changes in soil bacterial communities over time. This study provides the first insight into the relative contributions of different bacterial community assembly processes in soils upon antibiotic exposure at environmentally relevant concentrations.

Mechanistic insights into dissolved organic matter-driven protistan and bacterial community dynamics influenced by vegetation restoration

Vegetation restoration projects can not only improve water quality by absorbing and transferring pollutants and nutrients from non-vegetation sources, but also protect biodiversity by providing habitat for biological growth. However, the mechanism of the protistan and bacterial assembly processes in the vegetation restoration project were rarely explored. To address this, based on 18 S rRNA and 16 S rRNA high-throughput sequencing, we investigated the mechanism of protistan and bacterial community assembly processes, environmental conditions, and microbial interactions in the rivers with (out) vegetation restoration. The results indicated that the deterministic process dominated the protistan and bacterial community assembly (94.29% and 92.38%), influenced by biotic and abiotic factors. For biotic factors, microbial network connectivity was higher in the vegetation zone (average degree = 20.34) than in the bare zone (average degree = 11.00). For abiotic factors, the concentration of dissolved organic carbon ([DOC]) was the most important environmental factor affecting the microbial community composition. [DOC] was lower significantly in vegetation zone (18.65 ± 6.34 mg/L) than in the bare zone (28.22 ± 4.82 mg/L). In overlying water, vegetation restoration upregulated the protein-like fluorescence components (C1 and C2) by 1.26 and 1.01-folds and downregulated the terrestrial humic-like fluorescence components (C3 and C4) by 0.54 and 0.55-folds, respectively. The different DOM components guided bacteria and protists to select different interactive relationships. The protein-like DOM components led to bacterial competition, whereas the humus-like DOM components resulted in protistan competition. Finally, the structural equation model was established to explain that DOM components can affect protistan and bacterial diversity by providing substrates, facilitating microbial interactions, and promoting nutrient input. In general, our study provides insights into the responses of vegetation restored ecosystems to the dynamics and interactives in the anthropogenically influenced river and evaluates the ecological restoration performance of vegetation restoration from a molecular biology perspective.

Aerobic composting with sauerkraut fermentation waste water: Increasing the stability and complexity of bacterial community and changing bacterial community assembly processes

Aerobic composting renders the sauerkraut fermentation waste water harmless while adding soluble nutrients. Unravelling the bacterial community assembly processes, changes in community robustness and community cohesion and the relationship between them under composting treatment of sauerkraut fermentation waste water is an interesting topic. Sauerkraut fermentation waste water was used for composting, which increased bacterial linkages, community robustness, competitive behaviour during warming periods and cooperative behaviour during cooling periods, and the control of community assembly processes shifts from deterministic processes (variable selection) to stochastic processes (decentralised limitation). At the same time, the influence of community robustness and community cohesion on community assembly processes was increased. Community cohesion and robustness were significantly correlated with community function. These results indicate that community robustness and community cohesion are critical for the biological handling of hazardous substances.

Homogeneous Environmental Selection Structures the Bacterial Communities of Benthic Biofilms in Proglacial Floodplain Streams.

In proglacial floodplains, glacier recession promotes biogeochemical and ecological gradients across relatively small spatial scales. The resulting environmental heterogeneity induces remarkable microbial biodiversity among proglacial stream biofilms. Yet the relative importance of environmental constraints in forming biofilm communities remains largely unknown. Extreme environmental conditions in proglacial streams may lead to the homogenizing selection of biofilm-forming microorganisms. However, environmental differences between proglacial streams may impose different selective forces, resulting in nested, spatially structured assembly processes. Here, we investigated bacterial community assembly processes by unraveling ecologically successful phylogenetic clades in two stream types (glacier-fed mainstems and non-glacier-fed tributaries) draining three proglacial floodplains in the Swiss Alps. Clades with low phylogenetic turnover rates were present in all stream types, including Gammaproteobacteria and Alphaproteobacteria, while the other clades were specific to one stream type. These clades constituted up to 34.8% and 31.1% of the community diversity and up to 61.3% and 50.9% of the relative abundances in mainstems and tributaries, respectively, highlighting their importance and success in these communities. Furthermore, the proportion of bacteria under homogeneous selection was inversely related to the abundance of photoautotrophs, and these clades may therefore decrease in abundance with the future "greening" of proglacial habitats. Finally, we found little effect of physical distance from the glacier on clades under selection in glacier-fed streams, probably due to the high hydrological connectivity of our study reaches. Overall, these findings shed new light on the mechanisms of microbial biofilm assembly in proglacial streams and help us to predict their future in a rapidly changing environment. IMPORTANCE Streams draining proglacial floodplains harbor benthic biofilms comprised of diverse microbial communities. These high-mountain ecosystems are rapidly changing with climate warming, and it is therefore critical to better understand the mechanisms underlying the assembly of their microbial communities. We found that homogeneous selection dominates the structuring of bacterial communities in benthic biofilms in both glacier-fed mainstems and nonglacier tributary streams within three proglacial floodplains in the Swiss Alps. However, differences between glacier-fed and tributary ecosystems may impose differential selective forces. Here, we uncovered nested, spatially structured assembly processes for proglacial floodplain communities. Our analyses additionally provided insights into linkages between aquatic photoautotrophs and the bacterial taxa under homogeneous selection, potentially by providing a labile source of carbon in these otherwise carbon-deprived systems. In the future, we expect a shift in the bacterial communities under homogeneous selection in glacier-fed streams as primary production becomes more important and streams become "greener".

Soil bacterial community structure and functions but not assembly processes are affected by the conversion from monospecific Cunninghamia lanceolata plantations to mixed plantations

Forest conversion from monoculture plantations to mixed plantations has profound effects on ecological functions as well as soil bacterial community structure, and the creation of mixed plantations may substantially increase soil bacterial diversity. However, the potential function of soil nitrogen (N) cycling and the soil bacterial community assembly altered by forest conversion remain poorly understood. At Meicheng Forest Farm in 2018, we investigated the impacts of forest conversion on soil bacterial compositions and functions related to N cycling, bacterial networks, and assembly processes. The results showed that (1) soil bacterial composition and β diversity, but not α diversity, were significantly influenced by forest management practices; (2) forest conversion had profound effects on N cycling processes, especially N fixation, including the abundance of the N-fixing genera Bradyrhizobium, Burkholderia, and Geobacter, which increased in the mixed plantations; (3) bacterial network analysis showed that keystone taxa (i.e., Gemmatimonas in the mixed plantations and Gp2 in the pure plantations) might play key roles in bacterial networks, and mixed plantations seemed to have more complex network structures; and (4) stochastic processes, especially ecological drift, were predominant in bacterial community assembly processes, which remained unchanged under different management practices. Soil pH may affect bacterial community assembly processes. Overall, our study revealed distinct patterns of soil microbial compositions, especially among N cycling-related bacteria, between different forest management practices and further enhanced our understanding of how forest conversion affects potential microbial functioning and assembly processes.

Genomic and Environmental Factors Shape the Active Gill Bacterial Community of an Amazonian Teleost Holobiont.

Fish bacterial communities provide functions critical for their host's survival in contrasting environments. These communities are sensitive to environmental-specific factors (i.e., physicochemical parameters, bacterioplankton), and host-specific factors (i.e., host genetic background). The relative contribution of these factors shaping Amazonian fish bacterial communities is largely unknown. Here, we investigated this topic by analyzing the gill bacterial communities of 240 wild flag cichlids (Mesonauta festivus) from 4 different populations (genetic clusters) distributed across 12 sites in 2 contrasting water types (ion-poor/acidic black water and ion-rich/circumneutral white water). Transcriptionally active gill bacterial communities were characterized by a 16S rRNA metabarcoding approach carried on RNA extractions. They were analyzed using comprehensive data sets from the hosts genetic background (Genotyping-By-Sequencing), the bacterioplankton (16S rRNA) and a set of 34 environmental parameters. Results show that the taxonomic structure of 16S rRNA gene transcripts libraries were significantly different between the 4 genetic clusters and also between the 2 water types. However, results suggest that the contribution of the host's genetic background was relatively weak in comparison to the environment-related factors in structuring the relative abundance of different active gill bacteria species. This finding was also confirmed by a mixed-effects modeling analysis, which indicated that the dissimilarity between the taxonomic structure of bacterioplanktonic communities possessed the best explicative power regarding the dissimilarity between gill bacterial communities' structure, while pairwise fixation indexes (FST) from the hosts' genetic data only had a weak explicative power. We discuss these results in terms of bacterial community assembly processes and flag cichlid fish ecology. IMPORTANCE Host-associated microbial communities respond to factors specific to the host physiology, genetic backgrounds, and life history. However, these communities also show different degrees of sensitivity to environment-dependent factors, such as abiotic physico-chemical parameters and ecological interactions. The relative importance of host- versus environment-associated factors in shaping teleost bacterial communities is still understudied and is paramount for their conservation and aquaculture. Here, we studied the relative importance of host- and environment-associated factors structuring teleost bacterial communities using gill samples from a wild Amazonian teleost model (Mesonauta festivus) sampled in contrasting habitats along a 1500 km section of the Amazonian basin, thus ensuring high genetic diversity. Results showed that the contribution of the host's genetic background was weak compared to environment-related bacterioplanktonic communities in shaping gill bacterial assemblages, thereby suggesting that our understanding of teleost microbiome assembly could benefit from further studies focused on the ecological interplay between host-associated and free-living communities.