Community assembly of bacteria and archaea in coastal waters governed by contrasting mechanisms: A seasonal perspective

Seasonal dynamics of the microbial community in a strong-flavor baijiu fermentation

BACKGROUND

The microbial community plays a crucial role in Chinese strong-flavor baijiu (SFB) fermentation. However, the seasonal dynamics of the microbial community in the SFB fermentation system and its contribution to the unique flavor of SFB have not been fully elucidated. In this study, we investigated the seasonal dynamics of the microbial community through 16S rRNA and ITS gene sequencing.

RESULTS

The results revealed significant temporal dynamics of microbial communities and environmental variables throughout the four seasons. The influence of seasons on fungal communities was found to be more significant than on bacterial communities. The diversity of bacteria was higher during the winter and summer, whereas fungal diversity was more prominent in summer and autumn. Stochastic processes maintained their dominance in microbial assembly throughout all four seasons but the significance of heterogeneous selection increased during summer for both bacteria and fungi, whereas homogeneous selection became more pronounced during winter for fungi. The pH and environmental temperature were important drivers of microbial community assembly across different seasons, primarily impacting the core genera responsible for the production of major volatile flavor compounds (VFCs), especially ethyl caproate.

CONCLUSION

These findings provide new insights into the impact of seasons on microbial communities and hold promise for improving the quality-control measures for SFB brewed in different seasons. © 2024 Society of Chemical Industry.

Multidimensional aspects of riverine biodiversity can vary in response to nutrient pollution and environmental dynamics across climatic watersheds

The concurrent impact of anthropogenic and bioclimatic factors on biodiversity is a key focus in macroecological and biogeographical considerations in conservation programs within riverine ecosystems. However, there is still a lack of understanding about how multidimensional alpha and beta diversity measures respond to anthropogenic and bioclimatic drivers. Here, we assess the variations in taxonomic, phylogenetic, and functional alpha and beta diversity of riverine macroinvertebrate communities across different watersheds in China. Our results show significant declines in most facets of alpha diversity across watersheds with low environmental heterogeneity, reflecting the loss of species with unique traits and evolutionary legacies. Both functional and phylogenetic beta-diversity values reveal a decreasing pattern along low heterogeneity environments, whereas taxonomic beta-diversity shows a contrasting pattern, which highlights the influence of microhabitat variation. Moreover, our findings identify nutrient levels, organic matter, water quality indicators, climatic variation, and geographic and habitat characteristics as key determinants of diversity patterns that are indicative of broader water pollution challenges. These factors jointly influence functional and phylogenetic alpha diversity and contribute to spatial homogenization, which is reflected in decreased functional and phylogenetic beta diversity. These trends highlight the complex interactions of chemical and physical factors in shaping biodiversity characteristics across watersheds. Based on the null model, macroinvertebrate communities primarily show random patterns, whereas clustering and overdispersion were sporadically observed in specific communities. We propose that conservation and restoration efforts should be aimed at enhancing aquatic biomes by managing extreme environmental conditions and amplifying spatial spillover, thereby supporting the intrinsic dynamics within natural metasystems and thus preserving the multidimensional aspects of biodiversity.

Biogeography and dynamics of prokaryotic and microeukaryotic community assembly across 2600 km in the coastal and shelf ecosystems of the China Seas

Marine prokaryotes and microeukaryotes are essential components of microbial food webs, and drive the biogeochemical cycling. However, the underlying ecological mechanisms driving prokaryotic and microeukaryotic community assembly in large-scale coastal ecosystems remain unclear. In this study, we studied biogeographic patterns of prokaryotic and microeukaryotic communities in the coastal and shelf ecosystem of the China Seas. Results showed that prokaryotic richness was the highest in the Yangtze River Plume, whereas microeukaryotic richness decreased from south to north. Prokaryotic-microeukaryotic co-occurrence networks display greater complexity in the Yangtze River Plume compared to other regions, potentially indicating higher environmental heterogeneity. Furthermore, the cross-domain networks revealed that prokaryotes were more interconnected with each other than with microeukaryotes or between microeukaryotes, and all hub nodes were bacterial taxa, suggesting that prokaryotes may be more important for sustaining the stability and multifunctionality of coastal ecosystem than microeukaryotes. Variation Partitioning Analysis revealed that approximately equal proportions of environmental, biotic and spatial factors contribute to variations in microbial community composition. Temperature was the primary environmental driver of both prokaryotic and microeukaryotic communities across the China Seas. Additionally, stochastic processes (dispersal limitation) and deterministic processes (homogeneous selection) were two major ecological factors in shaping microeukaryotic and prokaryotic assemblages, respectively, suggesting their different environmental plasticity and evolutionary mechanisms. Overall, these results demonstrate both prokaryotic and microeukaryotic communities displayed a latitude-driven distribution pattern and different assembly mechanisms, improving our understanding of microbial biogeography patterns under global change and anthropogenic activity driven habitat diversification in the coastal and shelf ecosystem.

The ecology of the sewer systems: Microbial composition, function, assembly, and network in different spatial locations

Microbial induced concrete corrosion (MICC) is the primary deterioration affecting global sewers. Disentangling ecological mechanisms in the sewer system is meaningful for implementing policies to protect sewer pipes using trenchless technology. It is necessary to understand microbial compositions, interaction networks, functions, alongside assembly processes in sewer microbial communities. In this study, sewer wastewater samples and microbial samples from the upper part (UP), middle part (MP) and bottom part (BP) of different pipes were collected for 16S rRNA gene amplicon analysis. It was found that BP harbored distinct microbial communities and the largest proportion of unique species (1141) compared to UP and MP. The community in BP tended to be more clustered. Furthermore, significant differences in microbial functions existed in different spatial locations, including the carbon cycle, nitrogen cycle and sulfur cycle. Active microbial sulfur cycling indicated the corrosion risk of MICC. Among the environmental factors, the oxidation‒reduction potential drove changes in BP, while sulfate managed changes in UP and BP. Stochasticity dominated community assembly in the sewer system. Additionally, the sewer microbial community exhibited numerous positive links. BP possessed a more complex, modular network with higher modularity. These deep insights into microbial ecology in the sewer system may guide engineering safety and disaster prevention in sewer infrastructure.

Spatiotemporal dynamics of bacterioplankton communities in the estuaries of two differently contaminated coastal areas: Composition, driving factors and ecological process

Seasonal variations of environmental parameters usually lead to considerable changes in microbial communities. Nevertheless, the specific response patterns of these communities in coastal areas subjected to different levels of contamination remain unclear. Our results revealed notable fluctuations in the bacterioplankton community both seasonally and spatially, with seasonal variations being particularly significant. The diversity and composition of bacterioplankton communities in the estuaries varied significantly across seasons and between seas. Some bacterial phyla that were highly abundant in the dry season (e.g., Patescibacteria and Epsilonbacteraeota) were almost absent in the wet season. Furthermore, the network analysis revealed that the bacterioplankton networks were more complex during the wet season than in the dry season. In the wet season, the estuarine bacterioplankton network in the Yellow Sea region was more complex and stable, while the opposite was true in the dry season. According to the neutral community model, stochastic processes played a more significant role in the formation of bacterioplankton communities during the wet season than during the dry season. Estuarine bacterioplankton communities in the Yellow Sea region were more affected by stochastic processes compared to those in the Bohai Sea. In summary, in the estuaries of two differently contaminated coastal areas, the seasonal increase in nutrient levels enhanced the deterministic processes and network complexity of the bacterioplankton communities.

Role of keystone drives polycyclic aromatic hydrocarbons degradation and humification especially combined with aged contaminated soil in co-composting

Accumulation of persistent organic pollutants polycyclic aromatic hydrocarbons (PAHs) in soil has become a global problem. Composting is considered one of the more economical methods of soil remediation and is important for the resourceful use of wastes. Agroforestry waste is produced in huge amounts and is utilized at low rates, hence there is an urgent need to manage it. Here, leaf (LVS) or rice straw (SVS) was co-composting with aged contaminated soil to investigate bacteria interaction to PAHs degradation and humus formation. The degradation rate of high molecular weight PAHs (HMW-PAHs) in LVS and SVS reached 58.9% and 52.5%, and the low molecular weight PAHs (LMW-PAHs) were 77.5% and 65%. Meanwhile, the humus increased by 44.8% and 60.5% in LVS and SVS at the end of co-composting. The topological characteristics and community assembly of the bacterial community showed that LVS had higher complexity and more keystones than SVS, suggesting that LVS might more beneficial for the degradation of PAHs. The stability of the co-occurrence network and stochastic processes (dispersal limitation) dominated community assembly made SVS beneficial for humus formation. Mantel test and structural equation models indicated that the transformation of organic matter was important for PAHs degradation and humus formation. Degradation of HMW-PAHs led to bacterial succession, which affected the formation of precursors and ultimately increased the humus content. This study provided potential technology support for improving the quality of agroforestry organic waste composting and degrading PAHs in aged contaminated soil.

Seasonal dynamics of the microbial methane filter in the water column of a eutrophic coastal basin

In coastal waters, methane-oxidizing bacteria (MOB) can form a methane biofilter and mitigate methane emissions. The metabolism of these MOBs is versatile, and the resilience to changing oxygen concentrations is potentially high. It is still unclear how seasonal changes in oxygen availability and water column chemistry affect the functioning of the methane biofilter and MOB community composition. Here, we determined water column methane and oxygen depth profiles, the methanotrophic community structure, methane oxidation potential, and water-air methane fluxes of a eutrophic marine basin during summer stratification and in the mixed water in spring and autumn. In spring, the MOB diversity and relative abundance were low. Yet, MOB formed a methane biofilter with up to 9% relative abundance and vertical niche partitioning during summer stratification. The vertical distribution and potential methane oxidation of MOB did not follow the upward shift of the oxycline during summer, and water-air fluxes remained below 0.6 mmol m-2 d-1. Together, this suggests active methane removal by MOB in the anoxic water. Surprisingly, with a weaker stratification, and therefore potentially increased oxygen supply, methane oxidation rates decreased, and water-air methane fluxes increased. Thus, despite the potential resilience of the MOB community, seasonal water column dynamics significantly influence methane removal.

Stochasticity-driven weekly fluctuations distinguished the temporal pattern of particle-associated microorganisms from its free-living counterparts in temperate coastal seawater

Microbial community dynamics directly determine their ecosystem functioning. Despite the well-known annual recurrence pattern, little is known how different lifestyles affect the temporal variation and how community assembly mechanisms change over different temporal scales. Here, through a high-resolution observation of size fractionated samples over 60 consecutive weeks, we investigate the distinction in weekly distribution pattern and assembly mechanism between free-living (FL) and particle-associated (PA) communities in highly dynamic coastal environments. A clear pattern of annual recurrence was observed, which was more pronounced in FL compared to PA, resulting in higher temporal specificity in the former samples. Both the two size fractions displayed significant temporal distance-decay patterns, yet the PA community showed a higher magnitude of community variation between adjacent weeks, likely caused by sudden, drastic and long-lived blooms of heterotrophic bacteria. Generally, determinism (environmental selection) had a greater effect on the community assembly than stochasticity (random birth, death, and dispersal events), with significant contributions from temperature and inorganic nutrients. However, a clear shift in the temporal assembly pattern was observed, transitioning from a prevalence of stochastic processes driving short-term (within a month) fluctuations to a dominance of deterministic processes over longer time intervals. Between adjacent weeks, stochasticity was more important in the community assembly of PA than FL. This study revealed that stochastic processes can lead to rapid, dramatic and irregular PA community fluctuations, indicating weak resistance and resilience to disturbances, which considering the role of PA microbes in carbon processing would significantly affect the coastal carbon cycle. Our results provided a new insight into the microbial community assembly mechanisms in the temporal dimension.

Environmental gradients shape microbiome assembly and stability in the East China sea

Microbiomes play a key role in marine ecosystem functioning and sustainability. Their organization and stability in coastal areas, particularly in anthropogenic-influenced regions, however, remains unclear compared with an understanding of how microbial community shifts respond to marine environmental gradients. Here, the assembly and community associations across vertical and horizontal gradients in the East China Sea are systematically researched. The seawater microbial communities possessed higher robustness and lower fragmentation and vulnerability compared to the sediment microbiomes. Spatial gradients act as a deterministic filtering factor for microbiome organization. Microbial communities had lower phylogenetic distance and higher niche breadth in the nearshore and offshore areas compared to intermediate areas. The phylogenetic distance of microbiomes decreased from the surface to the bottom but the niche breadth was enhanced in surface and bottom environments. Vertical gradients destabilized microbial associations, while the community diversity was enhanced. Multivariate regression tree analysis and canonical correspondence analysis indicated that depth, distance from shore, nutrient availability, temperature, salinity, and chlorophyll a, affected the distribution and co-occurrence of microbial groups. Our results highlight the crucial roles of environmental gradients in determining microbiome association and stability. These results improve our understanding of the survival strategies/adaptive mechanisms of microbial communities in response to environmental variation and provide new insights for protecting the ecosystems and maintaining the sustainability of ecological functions.

Depth-Dependent Distribution of Prokaryotes in Sediments of the Manganese Crust on Nazimov Guyots of the Magellan Seamounts

Deep ocean polymetallic nodules, rich in cobalt, nickel, and titanium which are commonly used in high-technology and biotechnology applications, are being eyed for green energy transition through deep-sea mining operations. Prokaryotic communities underneath polymetallic nodules could participate in deep-sea biogeochemical cycling, however, are not fully described. To address this gap, we collected sediment cores from Nazimov guyots, where polymetallic nodules exist, to explore the diversity and vertical distribution of prokaryotic communities. Our 16S rRNA amplicon sequencing data, quantitative PCR results, and phylogenetic beta diversity indices showed that prokaryotic diversity in the surficial layers (0-8 cm) was > 4-fold higher compared to deeper horizons (8-26 cm), while heterotrophs dominated in all sediment horizons. Proteobacteria was the most abundant taxon (32-82%) across all sediment depths, followed by Thaumarchaeota (4-37%), Firmicutes (2-18%), and Planctomycetes (1-6%). Depth was the key factor controlling prokaryotic distribution, while heavy metals (e.g., iron, copper, nickel, cobalt, zinc) can also influence significantly the downcore distribution of prokaryotic communities. Analyses of phylogenetic diversity showed that deterministic processes governing prokaryotic assembly in surficial layers, contrasting with stochastic influences in deep layers. This was further supported from the detection of a more complex prokaryotic co-occurrence network in the surficial layer which suggested more diverse prokaryotic communities existed in the surface vs. deeper sediments. This study expands current knowledge on the vertical distribution of benthic prokaryotic diversity in deep sea settings underneath polymetallic nodules, and the results reported might set a baseline for future mining decisions.

Distinct patterns of distribution, community assembly and cross-domain co-occurrence of planktonic archaea in four major estuaries of China

BACKGROUND

Archaea are key mediators of estuarine biogeochemical cycles, but comprehensive studies comparing archaeal communities among multiple estuaries with unified experimental protocols during the same sampling periods are scarce. Here, we investigated the distribution, community assembly, and cross-domain microbial co-occurrence of archaea in surface waters across four major estuaries (Yellow River, Yangtze River, Qiantang River, and Pearl River) of China cross climatic zones (~ 1,800 km) during the winter and summer cruises.

RESULTS

The relative abundance of archaea in the prokaryotic community and archaeal community composition varied with estuaries, seasons, and stations (reflecting local environmental changes such as salinity). Archaeal communities in four estuaries were overall predominated by ammonia-oxidizing archaea (AOA) (aka. Marine Group (MG) I; primarily Nitrosopumilus), while the genus Poseidonia of Poseidoniales (aka. MGII) was occasionally predominant in Pearl River estuary. The cross-estuary dispersal of archaea was largely limited and the assembly mechanism of archaea varied with estuaries in the winter cruise, while selection governed archaeal assembly in all estuaries in the summer cruise. Although the majority of archaea taxa in microbial networks were peripherals and/or connectors, extensive and distinct cross-domain associations of archaea with bacteria were found across the estuaries, with AOA as the most crucial archaeal group. Furthermore, the expanded associations of MGII taxa with heterotrophic bacteria were observed, speculatively indicating the endogenous demand for co-processing high amount and diversity of organic matters in the estuarine ecosystem highly impacted by terrestrial/anthropogenic input, which is worthy of further study.

CONCLUSIONS

Our results highlight the lack of common patterns in the dynamics of estuarine archaeal communities along the geographic gradient, expanding the understanding of roles of archaea in microbial networks of this highly dynamic ecosystem.

Phylogenetic distance-decay patterns are not explained by local community assembly processes in freshwater lake microbial communities

While water and sediment microbial communities exhibit pronounced spatio-temporal patterns in freshwater lakes, the underlying drivers are yet poorly understood. Here, we evaluated the importance of spatial and temporal variation in abiotic environmental factors for bacterial and microeukaryotic community assembly and distance-decay relationships in water and sediment niches in Hongze Lake. By sampling across the whole lake during both Autumn and Spring sampling time points, we show that only bacterial sediment communities were governed by deterministic community assembly processes due to abiotic environmental drivers. Nevertheless, consistent distance-decay relationships were found with both bacterial and microeukaryotic communities, which were relatively stable with both sampling time points. Our results suggest that spatio-temporal variation in environmental factors was important in explaining mainly bacterial community assembly in the sediment, possibly due lesser disturbance. However, clear distance-decay patterns emerged also when the community assembly was stochastic. Together, these results suggest that abiotic environmental factors do not clearly drive the spatial structuring of lake microbial communities, highlighting the need to understand the role of other potential drivers, such as spatial heterogeneity and biotic species interactions.

Water table level controls methanogenic and methanotrophic communities and methane emissions in a Sphagnum-dominated peatland

Peatlands are important sources of the greenhouse gas methane emissions equipoised by methanogens and methanotrophs. However, knowledge about how microbial functional groups associated with methane production and oxidation respond to water table fluctuations has been limited to date. Here, methane-related microbial communities and the potentials of methane production and oxidation were determined along sectioned peat layers in a subalpine peatland across four Sphagnum-dominated sites with different water table levels. Methane fluxes were also monitored at these sites. The results showed that mcrA gene copies for methanogens were the highest in the 10- to 15-cm peat layer, which was also characterized by the maximum potential methane production (24.53 ± 1.83 nmol/g/h). Copy numbers of the pmoA gene for type Ia and Ib methanotrophs were enriched in the 0-5 cm peat layer with the highest potential methane oxidation (43.09 ± 3.44 nmol/g/h). For the type II methanotrophs, the pmoA gene copies were higher in the 10- to 15-cm peat layer. Hydrogenotrophic methanogens and type II methanotrophs dominated the methane functional groups. Deterministic process contributed more to methanogenic and methanotrophic community assemblages in comparison with stochastic process. The level of water table significantly shaped methanogenic and methanotrophic community structures and regulated methane fluxes. Compared with vascular plants, Sphagnum mosses significantly reduced the methane emissions in peatlands. Collectively, these findings enhance a comprehensive understanding of the effect of the water table level on methane functional groups, with consequential implications for reducing methane emissions within peatland ecosystems.IMPORTANCEThe water table level is recognized as a critical factor in regulating methane emissions, which are largely dependent on the balance of methanogens and methanotrophs. Previous studies on peat methane emissions have been mostly focused on spatial-temporal variations and the relationship with meteorological conditions. However, the role of the water table level in methane emissions remains unknown. In this work, four representative microhabitats along a water table gradient in a Sphagnum-dominated peatland were sampled to gain an insight into methane functional communities and methane emissions as affected by the water table level. The changes in methane-related microbial community structure and assembly were used to characterize the response to the water table level. This study improves the understanding of the changes in methane-related microbial communities and methane emissions with water table levels in peatlands.

Soil bacterial community composition is more stable in kiwifruit orchards relative to phyllosphere communities over time

BACKGROUND

Soil and phyllosphere (leaves and fruit) microbes play critical roles in the productivity and health of crops. However, microbial community dynamics are currently understudied in orchards, with a limited number incorporating temporal monitoring. We used 16S rRNA gene amplicon sequencing to investigate bacterial community temporal dynamics and community assembly processes on the leaves and fruit, and in the soil of 12 kiwifruit orchards across a cropping season in New Zealand.

RESULTS

Community composition significantly differed (P < 0.001) among the three sample types. However, the communities in the phyllosphere substrates more closely resembled each other, relative to the communities in the soil. There was more temporal stability in the soil bacterial community composition, relative to the communities residing on the leaves and fruit, and low similarity between the belowground and aboveground communities. Bacteria in the soil were more influenced by deterministic processes, while stochastic processes were more important for community assembly in the phyllosphere.

CONCLUSIONS

The higher temporal variability and the stochastic nature of the community assembly processes observed in the phyllosphere communities highlights why predicting the responsiveness of phyllosphere communities to environmental change, or the likelihood of pathogen invasion, can be challenging. The relative temporal stability and the influence of deterministic selection on soil microbial communities suggests a greater potential for their prediction and reliable manipulation.

Hydrodynamic and anthropogenic disturbances co-shape microbiota rhythmicity and community assembly within intertidal groundwater-surface water continuum

Tidal hydrodynamics drive the groundwater-seawater exchange and shifts in microbiota structure in the coastal zone. However, how the coastal water microbiota structure and assembly patterns respond to periodic tidal fluctuations and anthropogenic disturbance remains unexplored in the intertidal groundwater-surface water (GW-SW) continuum, although it affects biogeochemical cycles and coastal water quality therein. Here, through hourly time-series sampling in the saltmarsh tidal creek, rhythmic patterns of microbiota structure in response to daily and monthly tidal fluctuations in intertidal surface water are disentangled for the first time. The similarity in archaeal community structures between groundwater and ebb-tide surface water (R2=0.06, p = 0.2) demonstrated archaeal transport through groundwater discharge, whereas multi-source transport mechanisms led to unique bacterial biota in ebb-tide water. Homogeneous selection (58.6%-69.3%) dominated microbiota assembly in the natural intertidal GW-SW continuum and the presence of 157 rhythmic ASVs identified at ebb tide and 141 at flood tide could be attributed to the difference in environmental selection between groundwater and seawater. For intertidal groundwater in the tidal creek affected by anthropogenically contaminated riverine inputs, higher microbial diversity and shift in community structure were primarily controlled by increased co-contribution of dispersal limitation and drift (jointly 57.8%) and enhanced microbial interactions. Overall, this study fills the knowledge gaps in the tide-driven water microbial dynamics in coastal transition zone and the response of intertidal groundwater microbiota to anthropogenic pollution of overlying waters. It also highlights the potential of microbiome analysis in enhancing coastal water quality monitoring and identifying anthropogenic pollution sources (e.g., pathogenic Vibrio in aquaculture) through the detection of rhythmic microbial variances associated with intertidal groundwater discharge and seawater intrusion.

Spatial and Seasonal Patterns of Sediment Bacterial Communities in Large River Cascade Reservoirs: Drivers, Assembly Processes, and Co-occurrence Relationship

Sediment bacteria play an irreplaceable role in promoting the function and biogeochemical cycle of the freshwater ecosystem; however, little is known about their biogeographical patterns and community assembly mechanisms in large river suffering from cascade development. Here, we investigated the spatiotemporal distribution patterns of bacterial communities employing next-generation sequencing analysis and multivariate statistical analyses from the Lancang River cascade reservoirs during summer and winter. We found that sediment bacterial composition has a significant seasonal turnover due to the modification of cascade reservoirs operation mode, and the spatial consistency of biogeographical models (including distance-decay relationship and covariation of community composition with geographical distance) also has subtle changes. The linear regression between the dissimilarity of bacterial communities in sediments, geographical and environmental distance showed that the synergistic effects of geographical and environmental factors explained the influence on bacterial communities. Furthermore, the environmental difference explained little variations (19.40%) in community structure, implying the homogeneity of environmental conditions across the cascade reservoirs of Lancang River. From the quantification of the ecological process, the homogeneous selection was recognized as the dominating factor of bacterial community assembly. The co-occurrence topological network analyses showed that the key genera were more important than the most connected genera. In general, the assembly of bacterial communities in sediment of cascade reservoirs was mediated by both deterministic and stochastic processes and is always dominated by homogeneous selection with the seasonal switching, but the effects of dispersal limitation and ecological drift cannot be ignored.

Geographic Scale Influences the Interactivities Between Determinism and Stochasticity in the Assembly of Sedimentary Microbial Communities on the South China Sea Shelf

Determinism and stochasticity in microbial community composition decisions have attracted wide attention. However, there is no consensus on their interrelationships and relative importance, and the mechanism controlling the interaction between the two ecological processes remains to be revealed. The interaction of the two ecological processes on the continental shelf of the South China Sea was studied by performing 16S rRNA gene amplicon sequencing on 90 sediments at multiple depths in five sites. Three nearshore sites have higher microbial diversity than those two close to the shelf margin. Different microbial composition was observed between sites and microbial composition of nearshore sites was positively correlated with total nitrogen, total sulfur, total organic carbon, and dissolved oxygen, while that of offshore was positively correlated with total carbon, salinity, and photosynthetically active radiation. The null model test showed that the community composition among layers of the same site and between nearby sites was mainly dominated by the homogeneous selection, while that between distant sites was mainly affected by dispersal limitation, which indicates that geographic scale influences the interactivities of determinism and stochasticity. Our research indicates that the balance of these two ecological processes along the geographic scale is mainly determined by the dispersal ability of microbes and environmental heterogeneity between areas. The study provides new insights into how deterministic and stochastic processes shape microbial community composition on the continental shelf.

Seasonal variation significantly influenced the stochasticity of community assembly of amphibian symbiotic bacteria

Seasonal variation has been shown to influence symbiotic bacterial community composition and structure in amphibians. It is still unknown how the symbiotic bacterial community assembly changes during different seasons, especially for amphibians who are particularly sensitive to environmental change. We found significant differences in the composition and diversity (alpha and beta diversity) of amphibian skin and gut bacteria. Co-occurrences network analysis showed that seasonal variation reduced the microbial network complexity of amphibians from summer to autumn. The normalized stochastic ratio (NST) and phylogenetic bin-based null model analysis (iCAMP) models showed that the same result that stochastic processes was the major factor regulating the symbiotic bacterial community assembly mechanisms of amphibians. From summer to autumn, the symbiotic bacterial community assembly mechanisms declined in the contribution of stochastic processes, while increasing in the contribution of deterministic processes. Dispersal limitation was the dominant microbial assembly mechanism, followed by homogeneous selection, and then heterogeneous selection in the symbiotic bacterial community communities of amphibians between summer and autumn. Furthermore, higher niche width of the symbiotic bacterial community of amphibians was found in summer than autumn. Overall, these results demonstrated that seasonal variation influenced amphibian symbiotic bacterial community between summer and autumn.

Contrasting Community Assembly Mechanisms Underlie Similar Biogeographic Patterns of Surface Microbiota in the Tropical North Pacific Ocean

Marine microbiota are critical components of global biogeochemical cycles. However, the biogeographic patterns and ecological processes that structure them remain poorly understood, especially in the oligotrophic ocean. In this study, we used high-throughput sequencing of 16S and 18S rRNA genes to investigate the distribution patterns of bacterial and microeukaryotic communities and their assembly mechanisms in the surface waters of the tropical North Pacific Ocean. The fact that both the bacterial and the microeukaryotic communities showed similar distribution patterns (i.e., similar distance-decay patterns) and were clustered according to their geographic origin (i.e., the western tropical North Pacific and central tropical North Pacific) suggested that there was a significant biogeographic pattern of microbiota in the North Pacific Ocean. Indices of alpha diversity such as species richness, phylogenetic diversity, and the Shannon diversity index also differed significantly between regions. The correlations were generally similar between spatial and environmental variables and the alpha and beta diversities of bacteria and microeukaryotes across the entire region. The relative importance of ecological processes differed between bacteria and microeukaryotes: ecological drift was the principal mechanism that accounted for the structure of bacterial communities; heterogeneous selection, dispersal limitation, and ecological drift collectively explained much of the turnover of the microeukaryote communities.

IMPORTANCE Bacteria and microeukaryotes are extremely diverse groups in the ocean, where they regulate elemental cycling and energy flow. Studies of marine microbial ecology have benefited greatly from the rapid progress that has been made in genomic sequencing and theoretical microbial ecology. However, the spatial distribution of marine bacteria and microeukaryotes and the nature of the assembly mechanisms that determine their distribution patterns in oligotrophic marine waters are poorly understood. In this study, we used high-throughput sequencing methods to identify the distribution patterns and ecological processes of bacteria and microeukaryotes in an oligotrophic, tropical ocean. Our study showed that contrasting community assembly mechanisms underlaid similar biogeographic patterns of surface bacterial and microeukaryotic communities in the tropical North Pacific Ocean.

Diversity Distribution, Driving Factors and Assembly Mechanisms of Free-Living and Particle-Associated Bacterial Communities at a Subtropical Marginal Sea

Free-living (FL) and particle-associated (PA) bacterioplankton communities play critical roles in biogeochemical cycles in the ocean. However, their community composition, assembly process and functions in the continental shelf and slope regions are poorly understood. Based on 16S rRNA gene amplicon sequencing, we investigated bacterial communities’ driving factors, assembly processes and functional potentials at a subtropical marginal sea. The bacterioplankton community showed specific distribution patterns with respect to lifestyle (free living vs. particle associated), habitat (slope vs. shelf) and depth (surface vs. DCM and Bottom). Salinity and water temperature were the key factors modulating turnover in the FL community, whereas nitrite, silicate and phosphate were the key factors for the PA community. Model analyses revealed that stochastic processes outweighed deterministic processes and had stronger influences on PA than FL. Homogeneous selection (Hos) was more responsible for the assembly and turnover of FL, while drift and dispersal limitation contributed more to the assembly of PA. Importantly, the primary contributor to Hos in PA was Gammaproteobacteria:Others, whereas that in FL was Cyanobacteria:Bin6. Finally, the PICRUSt2 analysis indicated that the potential metabolisms of carbohydrates, cofactors, amino acids, terpenoids, polyketides, lipids and antibiotic resistance were markedly enriched in PA than FL.

Dredging alleviates cyanobacterial blooms by weakening diversity maintenance of bacterioplankton community

Disentangling ecological mechanisms behind dredging is meaningful to implement environmental policy for improving water quality. However, environmental adaptation and community assembly processes of bacterioplankton in response to dredging disturbance are poorly understood. Based on Illumine MiSeq sequencing and multiple statistical analyses, we estimated interactions, functions, environmental breadths, phylogenetic signals, phylogenetic clustering, and ecological assembly processes of bacterioplankton community before and after dredging. We found distinct change in community composition, comparable decreases in diversity, functional redundancy and conflicting interaction, relatively low phylogenetic clustering, and relatively weak environmental adaptation after dredging. The bacterioplankton community assembly was affected by both stochastic and deterministic processes before dredging, but dominated by stochasticity after dredging. Sediment total phosphorus was a decisive factor in balancing determinism and stochasticity for bacterioplankton community assembly before and after dredging. Consequently, taxonomic and phylogenetic α-diversities of bacterioplankton exhibited higher contributions to the water trophic level represented by chlorophyl α before dredging than afterwards. Our results emphasized bacterioplankton in response to environmental changes caused by dredging, with nutrient loss and ecological drift playing important roles. These findings extend knowledge of contribution of bacterioplankton diversity to water trophic level and decipher mechanisms of bacterioplankton diversity maintenance in response to dredging, which is useful for guiding mitigation of cyanobacterial blooms.

Groundwater bacterial communities evolve over time in response to recharge

Time series analyses are a crucial tool for uncovering the patterns and processes shaping microbial communities and their functions, especially in aquatic ecosystems. Subsurface aquatic environments are perceived to be more stable than surface oceans and lakes, due to the lack of sunlight, the absence of photosysnthetically-driven primary production, low temperature variations, and oligotrophic conditions. However, periodic groundwater recharge should affect the structure and succession of groundwater microbiomes. To disentangle the long-term temporal changes in bacterial communities of shallow fractured bedrock groundwater, and identify the drivers of the observed patterns, we analysed bacterial 16S rRNA gene sequencing data for samples collected monthly from three groundwater wells over a six-year period (n = 230) along a hillslope recharge area. We showed that the bacterial communities in the groundwater of limestone-mudstone alternations were not stable over time and exhibited non-linear dissimilarity patterns which corresponded to periods of groundwater recharge. Further, we observed an increase in dissimilarity over time (generalized additive model P < 0.001) indicating that the successive recharge events result in communities that are increasingly more dissimilar to the initial reference time point. The sampling period was able to explain up to 29.5% of the variability in bacterial community composition and the impact of recharge events on the groundwater microbiome was linked to the strength of the recharge and local environmental selection. Many groundwater bacteria originated from the recharge-related sources (mean = 66.5%, SD = 15.1%) and specific bacterial taxa were identified as being either enriched or repressed during recharge events. Overall, similar to surface aquatic environments, the microbiomes in shallow fractured-rock groundwater vary through time, though we revealed groundwater recharges as unique driving factors for these patterns. The high temporal resolution employed here highlights the dynamics of bacterial communities in groundwater, which is an essential resource for the provision of clean drinking water; understanding the biological complexities of these systems is therefore crucial.

Comparing Sediment Microbiomes in Contaminated and Pristine Wetlands along the Coast of Yucatan

Microbial communities are important players in coastal sediments for the functioning of the ecosystem and the regulation of biogeochemical cycles. They also have great potential as indicators of environmental perturbations. To assess how microbial communities can change their composition and abundance along coastal areas, we analyzed the composition of the microbiome of four locations of the Yucatan Peninsula using 16S rRNA gene amplicon sequencing. To this end, sediment from two conserved (El Palmar and Bocas de Dzilam) and two contaminated locations (Sisal and Progreso) from the coast northwest of the Yucatan Peninsula in three different years, 2017, 2018 and 2019, were sampled and sequenced. Microbial communities were found to be significantly different between the locations. The most noticeable difference was the greater relative abundance of Planctomycetes present at the conserved locations, versus FBP group found with greater abundance in contaminated locations. In addition to the difference in taxonomic groups composition, there is a variation in evenness, which results in the samples of Bocas de Dzilam and Progreso being grouped separately from those obtained in El Palmar and Sisal. We also carry out the functional prediction of the metabolic capacities of the microbial communities analyzed, identifying differences in their functional profiles. Our results indicate that landscape of the coastal microbiome of Yucatan sediment shows changes along the coastline, reflecting the constant dynamics of coastal environments and their impact on microbial diversity.

Stronger environmental adaptation of rare rather than abundant bacterioplankton in response to dredging in eutrophic Lake Nanhu (Wuhan, China)

Deciphering responses of rare versus abundant bacterioplankton to environmental change, crucial for understanding and mitigating of cyanobacterial blooms, is an important but poorly investigated subject. Using MiSeq sequencing, we investigated the taxonomic and phylogenetic diversity of rare and abundant bacterioplankton in eutrophic Lake Nanhu before and after dredging. We estimated environmental breadths and phylogenetic signals of ecological preferences of rare and abundant bacterioplankton, and investigated community function and bacterioplankton assembly processes. Both taxonomic and phylogenic distances of rare and abundant bacterioplankton communities were significantly positively correlated with the dissimilarity of environmental factors. Threshold indicator taxa analysis and Blomberg's K statistic indicated that rare taxa held broader environmental thresholds and stronger phylogenetic signals for ecological traits than abundant taxa. Environmental adaptations of both rare and abundant taxa exhibited distinct changes after dredging. Higher functional redundancy occurred in the abundant compared to the rare bacterioplankton, with functions of rare bacterioplankton decreasing and for the abundant ones increasing after dredging. The null model revealed that dispersal limitation belonging to stochastic processes determined the abundant bacterioplankton community assembly, whereas variable selection belonging to deterministic processes drove the rare one. Rare bacterioplankton was more environmentally constrained than the abundant one. Dissolved oxygen was the decisive factor in determining the balance between stochasticity and determinism in both rare and abundant bacterioplankton. Our study extends our knowledge of environmental adaptation of rare versus abundant bacterioplankton to massive disturbing measures, i.e. dredging, and allows to estimate dredging performance for mitigating cyanobacterial blooms from a molecular ecology viewpoint.