Phylogenetic shifts of bacterioplankton community composition along the Pearl Estuary: the potential impact of hypoxia and nutrients

Microbial community diversity from nearshore to offshore in the East China Sea

The Pollution Nagasaki (PN) section of the East China Sea (ECS) is a typical area for studying the complex hydrographic dynamics between Changjiang River discharge and Kuroshio, displaying intense variations of environmental gradients from nearshore to offshore. However, the temporal and spatial changes of microbial communities along the PN section have long been overlooked. In this study, we performed a comprehensive investigation into the abundance, diversity and ecology of free-living (FL) and particle-associated (PA) microbial communities in seawater samples along the PN section during both summer and winter. Distinct hydrological conditions and resulting environmental gradients were observed between summer and winter, with clear features of intrusive Kuroshio subsurface water in summer and strong vertical mixing of seawater in winter. Bacterial abundance along the PN section was higher in summer (1.11 × 108 copies·L-1 - 7.37 × 108 copies·L-1) than in winter (1.83 × 106 copies·L-1 - 1.34 × 108 copies·L-1). Microbial diversity, as indicated by α-diversity indices, remained at relatively stable levels in summer, while a clear decreasing trend was observed in winter along the PN section. Additionally, the winter communities exhibited a more evident spatial shift along the PN section compared to the summer communities. 16S rRNA gene amplicon sequencing showed that microbial community composition varied considerably between different seasons (summer and winter) and lifestyles (FL and PA), with a notable dominance of Ralstonia species. in winter. Regarding the assembly of microbial communities, the stochastic process represented by dispersal limitation was the dominant process in summer, while the deterministic homogeneous selection was the most important process in winter. Correspondingly, distinct topological properties of the microbial co-occurrence networks were shown between different seasons and along the PN section. These results enhance our understanding of how hydrological conditions influence dynamic changes of microbial communities along the PN section, providing new insights for the microbial community assembly and interactions in such a complex environment.

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.

Juvenile downstream migration patterns of an anadromous fish, allis shad (Alosa alosa), before and after the population collapse in the Gironde system, France

Diadromous fish have exhibited a dramatic decline since the end of the 20th century. The allis shad (Alosa alosa) population in the Gironde-Garonne-Dordogne (GGD) system, once considered as a reference in Europe, remains low despite a fishing ban in 2008. One hypothesis to explain this decline is that the downstream migration and growth dynamics of young stages have changed due to environmental modifications in the rivers and estuary. We retrospectively analysed juvenile growth and migration patterns using otoliths from adults caught in the GGD system 30 years apart during their spawning migration, in 1987 and 2016. We coupled otolith daily growth increments and laser ablation inductively-coupled plasma mass spectrometry measurements of Sr:Ca, Ba:Ca, and Mn:Ca ratios along the longest growth axis from hatching to an age of 100 days (i.e., during the juvenile stage). A back-calculation allowed us to estimate the size of juveniles at the entrance into the brackish estuary. Based on the geochemistry data, we distinguished four different zones that juveniles encountered during their downstream migration: freshwater, fluvial estuary, brackish estuary, and lower estuary. We identified three migration patterns during the first 100 days of their life: (a) Individuals that reached the lower estuary zone, (b) individuals that reached the brackish estuary zone, and (c) individuals that reached the fluvial estuary zone. On average, juveniles from the 1987 subsample stayed slightly longer in freshwater than juveniles from the 2016 subsample. In addition, juveniles from the 2016 subsample entered the brackish estuary at a smaller size. This result suggests that juveniles from the 2016 subsample might have encountered more difficult conditions during their downstream migration, which we attribute to a longer exposure to the turbid maximum zone. This assumption is supported by the microchemical analyses of the otoliths, which suggests based on wider Mn:Ca peaks that juveniles in 2010s experienced a longer period of physiological stress during their downstream migration than juveniles in 1980s. Finally, juveniles from the 2016 subsample took longer than 100 days to exit the lower estuary than we would have expected from previous studies. Adding a new marker (i.e., Ba:Ca) helped us refine the interpretation of the downstream migration for each individual.

Novel insights into the rhizosphere and seawater microbiome of Zostera marina in diverse mariculture zones

BACKGROUND

Seagrasses offer various ecosystem services and possess high levels of primary productivity. However, the development of mariculture has affected the homeostasis of seagrass meadow ecosystems. Plant-microbiome associations are essential for seagrasses health, but little is known about the role of environmental microbiomes and how they affect seagrass in a mariculture environment. In this study, we investigated the influence of mariculture on the rhizosphere and seawater microbiome surrounding Zostera marina and focused on the bacterial, eukaryotic, and fungal components in the composition, diversity, metabolism, and responses to mariculture-related environmental factors.

RESULTS

Significant differences in the composition, richness, diversity, and internal relations of the bacterial community between the seawater and rhizosphere sediment surrounding Z. marina were observed, while differences in the eukaryotic and fungal communities were less significant. More complex bacterial and fungal co-occurrence networks were found in the seawater and rhizosphere sediment of the Saccharina japonica (SJ) and sea cucumber (SC) culture zones. The seawater in the SJ zone had higher levels of dissimilatory and assimilatory nitrate reduction, denitrification, and nitrogen fixation processes than the other three zones. The assimilatory sulfate reduction enzymes were higher in the rhizosphere sediments of the SJ zone than in the other three zones. Tetracycline, sulfonamide, and diaminopyrimidine resistance genes were enriched in the mariculture SJ and SC zones.

CONCLUSIONS

Our findings might contribute to a better understanding of the effects of mariculture on the seagrass and the meadow ecosystems and thus revealing their potential operating mechanisms. These insights may serve to raise awareness of the effects of human activities on natural ecosystems, regulation of antibiotic usage, and environmental restoration. Video Abstract.

Active degradation-nitrification microbial assemblages in the hypoxic zone in a subtropical estuary

In 2017 summer, we observed widespread bottom hypoxia at the lower estuary of the Pearl River estuary (PRE). Our previous study noticed that AOA and bacteria were highly abundant and clustered within the hypoxia zone. Moreover, nitrification and respiration rates were also evidently higher in these hypoxic waters. These observations prompt us to investigate whether these two oxygen-consuming microorganisms have symbiotic relationships and whether specific groups consistently coexist and form ecological-meaningful associations. In this study, we use network analysis to investigate the presence and active communities (DNA-RNA) based on bacterial and AOA communities sequencing (inferred from the 16S rRNA and amoA gene, respectively) to gain more insight into ecological-meaningful associations. We observed a highly diverse and active bacterial community in the hypoxia zone. The RNA networks were more modulized than the corresponding DNA networks, indicating that the active communities were better parsed into functional microbial assemblages. The network topology revealed that Gammaproteobacteria, Bacteroidetes (Flavobacteriales), Alphaproteobacteria (Rhodobacterales and Rhodospirillales), Marinimicrobia, Cyanobacteria (Synechococcales), and AOA sublineages were module hubs and connectors, indicating that they were the keystone taxa of the microbial communities. The hub-subnetwork further showed robust co-occurrence between Gammaproteobacteria, Bacteroidetes (Flavobacteriales), Alphaproteobacteria (Rhodobacterales and Rhodospirillales), Marinimicrobia with AOA sublineages, and Nitrospinae (presumably NOB) reflecting the formation of Degradation-Nitrification (sequential oxidation of Organic matter degradation to ammonia, then nitrate) microbial assemblage in the hypoxia zone. The subnetworks revealed AOA ecotype-specific modularization and niche partitioning of different AOA sublineages. Interestingly, the recurring co-occurrence of nitrifiers assemblage in the RNA subnetworks (SCM1-like-II (AOA) and Nitrospinae OTUs (NOB) suggests an active interaction via nitrite exchange. The Degradation-Nitrification microbial assemblage may contribute substantially to the oxygen consumption in the hypoxia formation in PRE. Our results provide new insight into the functional microbial assemblages, which is worth further investigation on their ecological implication in estuarine waters.

Phylogenetically and metabolically diverse autotrophs in the world's deepest blue hole

The world's deepest yongle blue hole (YBH) is characterized by sharp dissolved oxygen (DO) gradients, and considerably low-organic-carbon and high-inorganic-carbon concentrations that may support active autotrophic communities. To understand metabolic strategies of autotrophic communities for obtaining carbon and energy spanning redox gradients, we presented finer characterizations of microbial community, metagenome and metagenome-assembled genomes (MAGs) in the YBH possessing oxic, hypoxic, essentially anoxic and completely anoxic zones vertically. Firstly, the YBH microbial composition and function shifted across the four zones, linking to different biogeochemical processes. The recovery of high-quality MAGs belonging to various uncultivated lineages reflected high novelty of the YBH microbiome. Secondly, carbon fixation processes and associated energy metabolisms varied with the vertical zones. The Calvin-Benson-Bassham (CBB) cycle was ubiquitous but differed in affiliated taxa at different zones. Various carbon fixation pathways were found in the hypoxic and essentially anoxic zones, including the 3-hyroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle affiliated to Nitrososphaeria, and Wood-Ljungdahl (WL) pathway affiliated to Planctomycetes, with sulfur oxidation and dissimilatory nitrate reduction as primary energy-conserving pathways. The completely anoxic zone harbored diverse taxa (Dehalococcoidales, Desulfobacterales and Desulfatiglandales) utilizing the WL pathway coupled with versatile energy-conserving pathways via sulfate reduction, fermentation, CO oxidation and hydrogen metabolism. Finally, most of the WL-pathway containing taxa displayed a mixotrophic lifestyle corresponding to flexible carbon acquisition strategies. Our result showed a vertical transition of microbial lifestyle from photo-autotrophy, chemoautotrophy to mixotrophy in the YBH, enabling a better understanding of carbon fixation processes and associated biogeochemical impacts with different oxygen availability.

Seasonal dynamics of bacterial community and co-occurrence with eukaryotic phytoplankton in the Pearl River Estuary

In this study, we investigated the taxonomic composition of the bacteria and phytoplankton communities in the Pearl River Estuary (PRE) through Illumina sequencing of the V3-V4 region of the 16 S rRNA gene. Furthermore, their relationships as well as recorded environmental variables were explored by co-occurrence networks. Bacterial community composition was different in two size fractions, as well as along the salinity gradient across two seasons. Free-living (FL) communities were dominated by pico-sized Cyanobacteria (Synechococcus CC9902) while Exiguobacterium, Halomonas and Pseudomonas were predominantly associated with particle-associated (PA) lifestyle, and Cyanobium PCC-6307 exhibited seasonal shifts in lifestyles in different seasons. In wet season, bacterial community composition was characterized by abundance of Cyanobacteria, Actinobacteria, and Bacteroidetes, which were tightly linked with high riverine inflow. While in dry season, Proteobacteria increased in prevalence, especially for Psychrobacter, NOR5/OM60 clade and Pseudomonas, which were thrived in lower water temperature and higher salinity. Moreover, we discovered that differences between PA and FL composition were more significant in the wet season than in the dry season, which may be due to better nutritional conditions of particles (indicated by POC%) in the wet season and then attract more diverse PA populations. Based on the analysis of plastidial 16 S rRNA genes, abundant small-sized mixotrophic phytoplankton (Dinophyceae, Euglenida and Haptophyta) were identified in the PRE. The complexity of co-occurrence network increased from FL to PA fractions in both seasons, which suggested that suspended particles can provide ecological niches for particle-associated colonizers contributing to the maintenance of a more stable community structure. In addition, the majority of phytoplankton species exhibited positive co-occurrences with both other phytoplankton species and bacterial counterparts, indicating the mutual cooperation between phytoplankton assemblages and specific bacterial populations e likely benefited from phytoplankton-derived organic compounds. This study enhances our understanding of the seasonal and spatial dynamics of bacterial communities and their potential relationship with phytoplankton assembly in estuarine waters.

Vertical dynamics of free-living and particle-associated vibrio communities in the eastern tropical Indian Ocean

Members of the family Vibrionaceae (vibrios) are widely distributed in estuarine, offshore, and marginal seas and perform an important ecological role in the marine organic carbon cycle. Nevertheless, there is little knowledge about whether vibrios play ecological roles in the oligotrophic pelagic area, which occupies a larger water volume. In this study, we investigated the abundance, diversity, and composition of free-living and particle-associated vibrios and their relationships with environmental factors along the water depth in the eastern tropical Indian Ocean (ETIO). The abundance of vibrios in free-living fractions was significantly higher than that of particle-associated fractions on the surface. Still, both were similar at the bottom, indicating that vibrios may shift from free-living lifestyles on the surface to mixed lifestyles at the bottom. Vibrio-specific 16S rRNA gene amplicon sequencing revealed that Paraphotobacterium marinum and Vibrio rotiferianus were dominant species in the water column, and Vibrio parahaemolyticus (a clinically important pathogen) was recorded in 102 samples of 111 seawater samples in 10 sites, which showed significant difference from the marginal seas. The community composition also shifted, corresponding to different depths in the water column. Paraphotobacterium marinum decreased with depth, and V. rotiferianus OTU1528 was mainly distributed in deeper water, which significantly correlated with the alteration of environmental factors (e.g., temperature, salinity, and dissolved oxygen). In addition to temperature and salinity, dissolved oxygen (DO) was an important factor that affected the composition and abundance of Vibrio communities in the ETIO. Our study revealed the vertical dynamics and preferential lifestyles of vibrios in the ETIO, helping to fill a knowledge gap on their ecological distribution in oligotrophic pelagic areas and fully understanding the response of vibrios in a global warming environment.

Distinct stochastic processes drive bacterial community assembly and co-occurrence patterns with common antibiotic resistance genes in two highly urbanised coastal ecosystems of the Pearl River Estuary

To comprehensively elucidate the ecology of the bacterial community and antibiotic resistance genes (ARGs) in urbanised coastal ecosystems, this study investigated the variations of bacterial community and five common types of ARGs, the impacting factors and assembly of bacterial community, as well as their co-occurrence relationships in two ecosystems of the Pearl River Estuary (PRE). The bacterial community composition and structure of the nearshore ecosystem (NSE) and the eight mouths of the PRE (EPR) markedly differed, with 38 phyla shared between these two ecosystems. The abundances of 10 ARGs and bacterial community diversity were significantly higher in the EPR than NSE. Moreover, 67.82% and 27.82% of the variation in the bacterial community was explained by spatial (44.42%/8.63%) and environmental (23.40%/19.19%) variables in the NSE and EPR, respectively. Significant distance-decay patterns were observed, and distinct stochastic processes (undominated processes or dispersal limitation) dominated bacterial community assembly in the NSE and EPR. Furthermore, co-occurrence patterns showed significant positive correlations between 48/182 ASVs belonging to 6/15 bacterial phyla and 8/11 ARGs in the NSE/EPR, with six common dominant hosts. These results clarify the drivers and mechanism shaping the bacterial community, providing further proof for potential ARG bacterial hosts in urbanised estuarine ecosystems.

Linking Groundwater to Surface Discharge Ecosystems: Archaeal, Bacterial, and Eukaryotic Community Diversity and Structure in Quebec (Canada)

Aquifer systems are composed of water flowing from surface recharge areas, to the subsurface and back to the surface in discharge regions. Groundwater habitats harbor a large microbial biomass and diversity, potentially contributing to surface aquatic ecosystems. Although this contribution has been widely studied in marine environments, very little is known about the connection between underground and surface microbial communities in freshwater settings. Therefore, in this study, we used amplicon sequencing to analyze the archaeal, bacterial, and eukaryotic community diversity and structure in groundwater and surface water samples, spanning the vast regions of the Laurentides and Lanaudières in the Quebec province (Canada). Our results show significant differences between subsurface and surface taxa; with more fungi, Amoebozoa, and chemolithoautotrophic prokaryotes involved in nitrogen-, sulfur-, and iron-cycling dominating the underground samples; while algae, ciliates, methanogens, and Actinobacteria dominate the surface discharge waters. Microbial source tracking suggested that only a small portion of the microbial communities in the groundwater contributed to the surface discharge communities. However, many taxa were shared between both habitats, with a large range of functional diversity, likely explaining their survival in both subsurface and surface water ecosystems.

Plastisphere composition in a subtropical estuary: Influence of season, incubation time and polymer type on plastic biofouling

Plastics are abundant artificial substrates in aquatic systems that host a wide variety of organisms (the plastisphere), including potential pathogens and invasive species. Plastisphere communities have many complex, but not well-understood ecological interactions. It is pivotal to investigate how these communities are influenced by the natural fluctuations in aquatic ecosystems, especially in transitional environments such as estuaries. Further study is needed in sub-tropical regions in the Southern Hemisphere, where plastic pollution is ever increasing. Here we applied DNA-metabarcoding (16S, 18S and ITS-2) as well Scanning Electron Microscopy (SEM) to assess the diversity of the plastisphere in the Patos Lagoon estuary (PLE), South Brazil. Through a one-year in situ colonization experiment, polyethylene (PE) and polypropylene (PP) plates were placed in shallow waters, and sampled after 30 and 90 days within each season. Over 50 taxa including bacteria, fungi and other eukaryotes were found through DNA analysis. Overall, the polymer type did not influence the plastisphere community composition. However, seasonality significantly affected community composition for bacteria, fungi and general eukaryotes. Among the microbiota, we found Acinetobacter sp., Bacillus sp., and Wallemia mellicola that are putative pathogens of aquatic organisms, such as algae, shrimp and fish, including commercial species. In addition, we identified organisms within genera that can potentially degrade hydrocarbons (e.g. Pseudomonas and Cladosporium spp). This study is the first to assess the full diversity and variation of the plastisphere on different polymers within a sub-tropical southern hemisphere estuary, significantly expanding knowledge on plastic pollution and the plastisphere in estuarine regions.

Local-Scale Damming Impact on the Planktonic Bacterial and Eukaryotic Assemblages in the upper Yangtze River

Dam construction and impoundment cause discontinuities in the natural biophysical gradients in rivers. These discontinuities may alter distinctive habitats and different microbial community assembly mechanisms upstream and downstream of dams, which reflect the potential impacts of damming on riverine aquatic ecosystems. In this study, we investigated the planktonic microbial assemblages of three large dams in the upper Yangtze River by using high-throughput sequencing. The results revealed that the alpha diversity indexes increased downstream of the dams. In addition, more eukaryotic ASVs solely occurred downstream of the dams, which indicated that a large proportion of eukaryotes appeared downstream of the dams. The nonmetric multidimensional scaling analysis indicated that there was no obvious geographic clustering of the planktonic microbial assemblages among the different locations or among the different dams. However, the dam barriers changed dam-related variables (maximum dam height and water level) and local environmental variables (water temperature, DOC, etc.) that could possibly affect the assembly of the planktonic microbial communities that are closest to the dams. A co-occurrence network analysis demonstrated that the keystone taxa of the planktonic bacteria and eukaryotes decreased downstream of the dams. In particular, the keystone taxa of the eukaryotes disappeared downstream of the dams. The robustness analysis indicated that the natural connectivity of the microbial networks decreased more rapidly upstream of the dams, and the downstream eukaryotic network was more stable. In conclusion, damming has a greater impact on planktonic eukaryotes than on bacteria in near-dam areas, and planktonic microbial assemblages were more susceptible to the environmental changes. Our study provides a better understanding of the ecological effects of river damming.

The biogeography and co-occurrence network patterns of bacteria and microeukaryotes in the estuarine and coastal waters

Community and diversity shifts of bacteria and microeukaryotes with strong environmental and spatial variations have been unveiled in the Pearl River Estuary (PRE) and northern coastal part of South China Sea (SCS). However, it is not clear what the determining factors shape the microbial community and how the biotic interactions respond to the estuarine and oceanic environment. Here, we established the multiple regression models (MRM) and co-occurrence networks on microbial communities in PRE and SCS habitats. The results showed that there were significant differences of the abiotic factors affecting the bacterial and microeukaryotic communities between PRE and SCS habitats. Salinity explained the largest variations to the microbial community dissimilarities in PRE. Whereas spatial and environmental factors determined the microbial community dissimilarities in SCS. Positive relations between parasitic lineages (e.g. Perkinsea and Cercozoa) and algal taxa (Dinophyceae, Cryptophyta, Chlorophyta and Ochrophyta) dominated in the PRE network. While parasites Syndiniales positively correlated with other Syndiniales and protists in SCS. Strong positive associations among autotrophic and heterotrophic groups were revealed in both niches. Therefore, the biotic interactions are also important and may be responsible for the unexplained variations of the abiotic factors from MRM models. Microbial network in the PRE estuarine water had weakened resistance to environmental disturbances, while the SCS network had greater capacity to maintain network stability. This study shed light on the different mechanisms of abiotic and biotic factors in shaping the compositions of bacteria and microeukaryotes between PRE and SCS niches, and highlights the weakening effect of environmental disturbances on the microbial network stability.

Highly active bacterial DMSP metabolism in the surface microlayer of the eastern China marginal seas

The microbial cycling of dimethylsulfoniopropionate (DMSP) and the resulting gaseous catabolites dimethylsulfide (DMS) or methylmercaptan (MeSH) play key roles in the global sulfur cycle and potentially climate regulation. As the ocean-atmosphere boundary, the sea surface microlayer (SML) is important for the generation and emission of DMS and MeSH. However, understanding of the microbial DMSP metabolism remains limited in the SML. Here, we studied the spatiotemporal differences for DMS/DMSP, bacterial community structure and the key bacterial DMSP metabolic genes between SML and subsurface seawater (SSW) samples in the eastern China marginal seas (the East China Sea and Yellow Sea). In general, DMSP_d and DMSP_t concentrations, and the abundance of total, free-living and particle-associated bacteria were higher in SML than that in SSW. DMSP synthesis (~7.81-fold for dsyB, ~2.93-fold for mmtN) and degradation genes (~5.38-fold for dmdA, ~6.27-fold for dddP) detected in SML were more abundant compared with SSW samples. Free-living bacteria were the main DMSP producers and consumers in eastern Chinese marginal sea. Regionally, the bacterial community structure was distinct between the East China Sea and the Yellow Sea. The abundance of DMSP metabolic genes (dsyB, dmdA, and dddP) and genera in the East China Sea were higher than those of the Yellow Sea. Seasonally, DMSP/DMS level and DMSP metabolic genes and bacteria were more abundant in SML of the East China Sea in summer than in spring. Different from those in spring, Ruegeria was the dominant DMSP metabolic bacteria. In conclusion, the DMSP synthesis and degradation showed significant spatiotemporal differences in the SML of the eastern China marginal seas, and were consistently more active in the SML than in the SSW.

Bacterial Community Composition and Function of Tropical River Ecosystem along the Nandu River on Hainan Island, China

Microorganisms play a pivotal role in nutrient cycling in aquatic ecosystems. Understanding bacterial diversity and its functional composition are crucial for aquatic ecology and protection. We investigated the bacterial community structure using 16S rRNA gene amplicons high-throughput sequencing in this study. Results showed that 105 amplicon sequence variants (ASVs) account for 43.8% of the total sequences shared by the Nandu River's lower, middle, and upper reach and the Songtao Reservoir. The dominant bacterial phylum in the Nandu River and its connected Songtao Reservoir were Proteobacteria and Actinobacteriota, respectively. The highest Chao1 and Shannon index values were found in the lower reach of the Nandu River. Beta diversity analysis showed the divergence in bacterial communities in the Nandu River and Songtao Reservoir, but not in different reaches. Among the water properties, based on the Mantel test, dissolved oxygen, total nitrogen, and nitrite significantly affected the bacterial communities. The functional profiles predicted by Tax4Fun2 showed that metabolism was the most abundant function group. The relative abundance of genetic information processing was significantly higher in the Songtao Reservoir than in the Nandu River, while the relative abundance of human diseases was significantly lower in the Songtao Reservoir than in the Nandu River. The appearance of the xenobiotics biodegradation and metabolism function group requires us to pay more attention to possible water pollution, especially at the upper reach of the Nandu River.

Ecosystem size-induced environmental fluctuations affect the temporal dynamics of community assembly mechanisms

Understanding processes that determine community membership and abundance is important for many fields from theoretical community ecology to conservation. However, spatial community studies are often conducted only at a single timepoint despite the known influence of temporal variability on community assembly processes. Here we used a spatiotemporal study to determine how environmental fluctuation differences induced by mesocosm volumes (larger volumes were more stable) influence assembly processes of aquatic bacterial metacommunities along a press disturbance gradient. By combining path analysis and network approaches, we found mesocosm size categories had distinct relative influences of assembly process and environmental factors that determined spatiotemporal bacterial community composition, including dispersal and species sorting by conductivity. These processes depended on, but were not affected proportionately by, mesocosm size. Low fluctuation, large mesocosms primarily developed through the interplay of species sorting that became more important over time and transient priority effects as evidenced by more time-delayed associations. High fluctuation, small mesocosms had regular disruptions to species sorting and greater importance of ecological drift and dispersal limitation indicated by lower richness and higher taxa replacement. Together, these results emphasize that environmental fluctuations influence ecosystems over time and its impacts are modified by biotic properties intrinsic to ecosystem size.

Pathogenic bacteria significantly increased under oxygen depletion in coastal waters: A continuous observation in the central Bohai Sea

The spread of pathogenic bacteria in coastal waters endangers the health of the local people and jeopardizes the safety of the marine environment. However, their dynamics during seasonal hypoxia in the Bohai Sea (BHS) have not been studied. Here, pathogenic bacteria were detected from the 16S rRNA gene sequencing database and were used to explore their dynamics and driving factors with the progressively deoxygenating in the BHS. Our results showed that pathogenic bacteria were detected in all samples, accounting for 0.13 to 24.65% of the total number of prokaryotic sequences in each sample. Pathogenic Proteobacteria was dominated in all samples, followed by Firmicutes, Actinobacteria, Tenericutes, and Bacteroidetes, etc. β-diversity analysis showed that pathogenic bacteria are highly temporally heterogeneous and regulated by environmental factors. According to RDA analysis, these variations may be influenced by salinity, ammonia, DO, phosphate, silicate, and Chl a. Additionally, pathogenic bacteria in surface water and hypoxia zone were found to be significantly separated in August. The vertical distribution of pathogenic bacterial communities is influenced by several variables, including DO and nutrition. It is noteworthy that the hypoxia zones increase the abundance of certain pathogenic genera, especially Vibrio and Arcobacter, and the stability of the pathogenic bacterial community increased from May to August. These phenomena indicate that the central Bohai Sea is threatened by an increasingly serious pathogenic community from May to August. And the developing hypoxia zone in the future may intensify this phenomenon and pose a more serious threat to human health. This study provides new insight into the changes of pathogenic bacteria in aquatic ecosystems and may help to make effective policies to control the spread of pathogenic bacteria.

Seasonal Succession and Temperature Response Pattern of a Microbial Community in the Yellow Sea Cold Water Mass

Explaining the temporal dynamics of marine microorganisms is critical for predicting their changing pattern under environmental disturbances. Although the effect of temperature on microbial seasonality has been widely studied, the phylogenetic structure of the temperature response pattern and the extent to which temperature shift leads to disruptive community changes are still unclear. Here, we explored the microbial seasonal dynamics in the Yellow Sea Cold Water Mass (YSCWM) that occurs in summer and disappears in winter and tested the temperature thresholds and phylogenetic coherence in response to temperature change. The existence of YSCWM generates strong temperature gradients in summer and confers little temperature change during seasonal transition, thus representing a unique intermediate state. The microbial community of YSCWM is more similar to that in the previous YSCWM in winter than that outside YSCWM. Temperature alone explains >50% of the community variation, suggesting that a temperature shift can induce a nearly seasonality-level community variance in summer. Persistence of most previous winter YSCWM inhabitants in YSCWM leads to conservation in predicted functional potentials and cooccurrence patterns, indicating a decisive role of temperature in maintaining functionality. Evaluation of the temperature threshold reveals that a small temperature change can lead to significant community turnover, with most taxa negatively responding to an elevation in temperature. The temperature response pattern is phylogenetically structured, and closely related taxa show an incohesive response. Our study provides novel insights into microbial seasonality and into how marine microorganisms respond to temperature fluctuations. IMPORTANCE Microbial seasonality is driven by a set of covarying factors including temperature. There is still a lack of understanding of the details of the phylogenetic structure and susceptibility of microbial communities in response to temperature variation. Through examination of the microbial community in a seasonally occurring summer cold water mass, which experiences little temperature change during seasonal transition, we show here that the cold water mass leads to nearly seasonality-level variations in community composition and predicted functional profile in summer. Moreover, massive community turnover occurs within a small temperature shift, with most taxa decreasing in abundance in response to increased temperature, and contrasting response patterns are observed between phylogenetically closely related taxa. These results suggest temperature as the fundamental factor over other covarying factors in structuring microbial seasonality, providing important insights into the variation mode of the microbial community under temperature disturbances.

Eutrophic levels and algae growth increase emissions of methane and volatile sulfur compounds from lakes

Eutrophic lakes are hot spots of CH₄ and volatile sulfur compound (VSC) emissions, especially during algal blooms and decay. However, the response of CH₄ and VSC emissions to lake eutrophication and algae growth as well as the underlying mechanisms remain unclear. In this study, the emissions of CH₄ and VSCs from four regions of Lake Taihu with different eutrophic levels were investigated in four months (i.e., March, May, August and December). The CH₄ emissions ranged from 20.4 to 126.9 mg m^-2 d^-1 in the investigated sites and increased with eutrophic levels and temperature. H₂S and CS₂ were the dominant volatile sulfur compounds (VSCs) emitted from the lake. The CH₄ oxidation potential of water ranged from 2.1 to 14.9 μg h^-1 L^-1, which had positive correlations with trophic level index and the environmental variables except for the NH₄⁺-N concentration. Eutrophic levels could increase the abundances of bacteria and methanotrophs in lake water. α-Proteobacteria methanotroph Methylocystis was more abundant than γ-Proteobacteria methanotrophs in March and May, while the latter was more abundant in August and November. The relative abundance of Cyanobacteria, including Microcystis, A. granulata var. angustissima and Cyanobium had significantly positive correlations with temperature, turbidity, SO₄^2--S, and total sulfur. Partial least squares path modelling revealed that the algal growth could promote VSC emissions, which had a positive correlation with CH₄ oxidation potential, likely due to the positive correlation between the CH₄ and VSC emissions from lakes. These findings indicate that water eutrophication and algae growth could increase the emissions of CH₄ and VSCs from lakes. Controlling algae growth might be an effective way to mitigate the emissions of CH₄ and VSCs from freshwater lakes.

Understanding the Variation of Bacteria in Response to Summertime Oxygen Depletion in Water Column of Bohai Sea

Aiming to reveal the variation in bacteria community under oxygen depletion formed every summer in water column of central Bohai Sea, a time-scenario sampling from June to August in 2018 at a 20-day interval along one inshore-offshore transect was settled. Water samples were collected at the surface, middle, and bottom layer and then analyzed by high-throughput sequencing targeting both 16S rRNA and nosZ genes. Compared to the surface and middle water, oxygen depletion occurred at bottom layer in August. In top two layers, Cyanobacteria dominated the bacterial community, whereas heterotrophic bacteria became dominant in bottom water of Bohai Sea. Based on the time scenario, distinct community separation was observed before (June and July) and after (August) oxygen depletion (p = 0.003). Vertically, strict stratification of nosZ gene was stably formed along 3 sampling layers. As a response to oxygen depletion, the diversity indices of both total bacteria (16S rRNA) and nosZ gene-encoded denitrification bacteria all increased, which indicated the intense potential of nitrogen lose when oxygen depleted. Dissolved oxygen (DO) was the key impacting factor on the community composition of total bacteria in June, whereas nutrients together with DO play the important roles in August for both total and denitrifying bacteria. The biotic impact was revealed further by strong correlations which showed between Cyanobacteria and heterotrophic bacteria in June from co-occurrence network analysis, which became weak in August when DO was depleted. This study discovered the variation in bacteria community in oxygen-depleted water with further effort to understand the potential role of denitrifying bacteria under oxygen depletion in Bohai Sea for the first time, which provided insights into the microbial response to the world-wide expanding oxygen depletion and their contributions in the ocean nitrogen cycling.

Metagenomic insights into surface water microbial communities of a South Asian mangrove ecosystem

Estuaries are one of the most productive ecosystems and their productivity is maintained by resident microbial communities. Recent alterations driven by climate change have further escalated these stressors leading to the propagation of traits such as antibiotic resistance and heavy metal resistance in microbial communities. Surface water samples from eleven stations along the Thakuran and Matla estuaries of the Sundarbans Biosphere Reserve (SBR) of Sundarbans mangrove located in South Asia were sampled in monsoon (June) 2019 to elucidate resident microbial communities based on Nanopore sequencing. Metagenomic analyses revealed the widespread dominance of Proteobacteria across all the stations along with a high abundance of Firmicutes. Other phyla, including Euryarchaeota, Thaumarchaeota, Actinobacteria, Bacteroidetes and Cyanobacteria showed site-specific trends in abundance. Further taxonomic affiliations showed Gammaproteobacteria and Alphaproteobacteria to be dominant classes with high abundances of Bacilli in SBR_Stn58 and SBR_Stn113. Among the eukaryotic communities, the most abundant classes included Prasinophyceae, Saccharyomycetes and Sardariomycetes. Functional annotation showed metabolic activities such as carbohydrate, amino acid, nitrogen and phosphorus metabolisms to be uniformly distributed across all the studied stations. Pathways such as stress response, sulphur metabolism and motility-associated genes appeared in low abundances in SBR. Functional traits such as antibiotic resistance showed overwhelming dominance of genes involved in multidrug resistance along with widespread resistance towards commonly used antibiotics including Tetracycline, glycopeptide and aminoglycoside. Metal resistance genes including arsenic, nickel and copper were found in comparable abundances across the studied stations. The prevalence of ARG and MRG might indicate presence of pollutants and hint toward deteriorating ecosystem health status of Sundarbans mangrove.

Diversity Patterns of Protists Are Highly Affected by Methods Disentangling Biological Variants: A Case Study in Oligotrich (s.l.) Ciliates

Protists are a dominant group in marine microplankton communities and play important roles in energy flux and nutrient cycling in marine ecosystems. Environmental sequences produced by high-throughput sequencing (HTS) methods are increasingly used for inferring the diversity and distribution patterns of protists. However, studies testing whether methods disentangling biological variants affect the diversity and distribution patterns of protists using field samples are insufficient. Oligotrich (s.l.) ciliates are one group of the abundant and dominant planktonic protists in coastal waters and open oceans. Using oligotrich (s.l.) ciliates in field samples as an example, the present study indicates that DADA2 performs better than SWARM, UNOISE, UPARSE, and UCLUST for inferring diversity patterns of oligotrich (s.l.) ciliates in the Pearl River Estuary and surrounding regions. UPARSE and UNOISE might underestimate species richness. SWARM might not be suitable for the resolution of alpha diversity owing to its rigorous clustering and sensitivity to sequence variations. UCLUST with 99% clustering threshold overestimates species richness, and the beta diversity pattern inferred by DADA2 is more reasonable than that of the other methods. Additionally, salinity is shown to be one of the key factors responsible for variations in the community distribution of ciliates, but infrequent marine-freshwater transitions occurred during evolutionary terms of this group.

Response mechanism of microbial community to seasonal hypoxia in marine ranching

Seasonal hypoxia, as an increasingly recognized environmental issue, frequently occurred in marine ranching from northern Yellow Sea, China. Although microorganisms play an important ecological role in marine ecosystems, but little is known on the response mechanism of microbial community to seasonal hypoxia in marine ranching. A total of 132 seawater samples and 47 sediment samples were collected from the marine ranching, both in the death disaster zone of sea cucumbers and the non-disaster zone, and in different months. 16S rRNA gene high-throughput sequencing was used to explore the microbial community and its influencing factors. The results showed that the stratification in community composition and dissolved oxygen content appeared in August. The Alpha diversity in seawater was higher in summer than in winter, and significant differences in Beta diversity appeared between the death disaster zone of sea cucumbers and the non-disaster zone in sediments. In addition, environmental effects explained more of the variation in bacterial community composition in seawater as compared with spatial effects did, whereas, sedimentary bacterial communities were more closely related to spatial effects. The present results could provide fundamental data for understanding the response mechanism of the microbial community to seasonal hypoxia in marine ranching and are of great significance for the management and protection of marine ranching.

Seasonal shift of water quality in China Yangtze River and its impacts on membrane fouling development during the drinking water supply by membrane distillation system

Membrane distillation (MD) technique is increasingly regarded as a promising process for drinking water supply and wastewater treatment owing to its great water purification and usage of renewable energy. Like other membrane separation processes, the membrane fouling issue is widely considered as the main obstacle for real applications of large-scale MD systems. Feedwater characteristics, as the predominant factors for membrane fouling layer formation, mostly determined the membrane fouling trend of MD. Thus the impacts of seasonal shifts of initial feedwater quality on the MD membrane fouling were detailedly researched in this study, and the biofilm development mechanism was especially explored. The bacterial community structure of membrane biofilms was clearly clarified in MD runs of Yangtze River waters that collected in four seasons. The results revealed that the winter run posed a quite sharp flux drop, while a relatively milder flux decline behaviour was seen for other groups despite of the higher bacteria concentration of initial feedwaters. The poorer water quality in winter induced the establishment of a rather thick biofilm on the MD membrane, in which the biofilm-forming bacteria (Gammaproteobacteria and Alphaproteobacteria) and organic matters (EPS) were remarkably observed. Comparatively, a relatively thin biofilm containing abundant live cells and fewer organics finally formed in summer and autumn runs, causing a mitigated flux decline trend. Hence, it can be inferred that the membrane flux decline of MD was likely to be more sensitive to the organic attachment on the membrane in comparison with the bacteria adhesion. Finally, a three-phase pretreatment method was suggested for MD fouling control, including heating course, sterilization course, and filtration course.

Salinity Gradient Controls Microbial Community Structure and Assembly in Coastal Solar Salterns

Salinity acts as a critical environmental filter on microbial communities in natural systems, negatively affecting microbial diversity. However, how salinity affects microbial community assembly remains unclear. This study used Wendeng multi-pond saltern as a model to evaluate the prokaryotic community composition and diversity and quantify the relative importance of ecological processes across salinity gradients. The results showed that low-saline salterns (45–80 g/L) exhibited higher bacterial diversity than high-saline salterns (175–265 g/L). The relative abundance of taxa assigned to Halomicrobiaceae, Rhodobacteraceae, Saprospiraceae, and Thiotrichaceae exhibited a hump-shaped dependence on increasing salinity. Salinity and pH were the primary environmental factors that directly or indirectly determined the composition and diversity of prokaryotic communities. Microbial co-occurrence network dynamics were more complex in the sediment than in the water of salterns. An infer Community Assembly Mechanisms by Phylogenetic-bin-based null model analysis (iCAMP) showed that microbial community assembly in sediment and water differed. Our findings provide more information about microbial community structure and the importance of various ecological processes in controlling microbial community diversity and succession along salinity gradients in water and sediment.

Spatio-temporal variation of bacterioplankton community structure in the Pearl River: impacts of artificial fishery habitat and physicochemical factors

Background

Artificial fishery habitat has been widely used in fishery resource protection and water habitat restoration. Although the bacterioplankton plays an important ecological role in fisheries ecosystems, the effect of artificial fishery habitat on bacterioplankton is not clear. In this study, high-throughput sequencing based on the 16S rRNA gene was carried out to study the characteristics of bacterioplankton community structure in artificial fishery habitat and to determine the principal environmental factors that shaped the composition, structure and function of bacterioplankton communities in an unfed aquaculture system.

Results

The results indicated that the most dominant phyla were Proteobacteria (Alphaproteobacteria and Gammaproteobacteria), Actinobacteria, Cyanobacteria, and Bacteroidetes, which accounted for 28.61%, 28.37%, 19.79%, and 10.25% of the total abundance, respectively. The factors that cause the differences in bacterioplankton community were mainly manifested in three aspects, including the diversity of the community, the role of artificial fishery habitat, and the change of environmental factors. The alpha diversity analysis showed that the diversity and richness index of the bacterioplankton communities were the highest in summer, which indicated that the seasonal variation characteristics had a great influence on it. The CCA analysis identified that the dissolved oxygen, temperature, and ammonium salt were the dominant environmental factors in an unfed aquaculture system. The LEfSe analysis founded 37 indicator species in artificial structure areas (AS group), only 9 kinds existing in the control areas of the open-water group (CW group). Meanwhile, the KEGG function prediction analysis showed that the genes which were related to metabolism in group AS were significantly enhanced.

Conclusions

This study can provide reference value for the effect of artificial habitat on bacterioplankton community and provide fundamental information for the follow-up study of ecological benefits of artificial fishery habitat. It may be contributed to apply artificial fishery habitat in more rivers.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-01965-3.

Biochar dose determines methane uptake and methanotroph abundance in Haplic Luvisol

Biochar promotes C sequestration and improvement of soil properties. Nevertheless, the effects of biochar addition on soil condition are poorly understood, especially with respect to greenhouse gas (GHG) emissions. A large proportion of GHG emissions derive from agriculture and, thus, recognition of the effect of biochar addition to soil on GHG emissions from terrestrial ecosystems is an important issue. The purpose of our study was to evaluate the short- and long-term effects of biochar application on soil in aspects of: GHG exchange (CH₄ and CO₂), basic physicochemical soil properties and structure of microbial communities in Haplic Luvisol. Soil was collected from fallow fields enriched with three doses of wood offcuts biochar (10, 20 and 30 Mg ha^-1) and incubated at two moisture levels (60 and 100% WHC) with the addition of 1% CH₄. To evaluate the influence of biochar aging in soil, the samples were analysed directly (short-term response) and five years (long-term response) after amendment. Generally, biochar addition increased soil pH, redox potential (Eh), organic carbon (SOC) and dissolved organic carbon (DOC) contents. Under 60% WHC, direct biochar application to the soil resulted in a clear improvement in the CH₄ uptake rate. In contrast to that (at 100% WHC) methane uptake rates were twofold decreased. The positive effect was reduced due to biochar aging in the soil, but five years after application, at 60% WHC and the highest biochar dose (30 Mg ha^-1) still significantly enhanced CH₄ oxidation. From a short-term perspective, biochar application increased CO₂ emissions, but after five years this effect was not observed. Microbial tests confirmed that the improvement in CH₄ oxidation was correlated with methanotroph abundance in the soil. Moreover, an increase of Methylocystis abundance in the soil enriched with biochar along with enhanced CH₄ uptake rates confirm the positive biochar influence on methanotrophic communities.

Estuarine gradients dictate spatiotemporal variations of microbiome networks in the Chesapeake Bay

BACKGROUND

Annually reoccurring microbial populations with strong spatial and temporal variations have been identified in estuarine environments, especially in those with long residence time such as the Chesapeake Bay (CB). However, it is unclear how microbial taxa cooccurr and how the inter-taxa networks respond to the strong environmental gradients in the estuaries.

RESULTS

Here, we constructed co-occurrence networks on prokaryotic microbial communities in the CB, which included seasonal samples from seven spatial stations along the salinity gradients for three consecutive years. Our results showed that spatiotemporal variations of planktonic microbiomes promoted differentiations of the characteristics and stability of prokaryotic microbial networks in the CB estuary. Prokaryotic microbial networks exhibited a clear seasonal pattern where microbes were more closely connected during warm season compared to the associations during cold season. In addition, microbial networks were more stable in the lower Bay (ocean side) than those in the upper Bay (freshwater side). Multivariate regression tree (MRT) analysis and piecewise structural equation modeling (SEM) indicated that temperature, salinity and total suspended substances along with nutrient availability, particulate carbon and Chl a, affected the distribution and co-occurrence of microbial groups, such as Actinobacteria, Bacteroidetes, Cyanobacteria, Planctomycetes, Proteobacteria, and Verrucomicrobia. Interestingly, compared to the abundant groups (such as SAR11, Saprospiraceae and Actinomarinaceae), the rare taxa including OM60 (NOR5) clade (Gammaproteobacteria), Micrococcales (Actinobacteria), and NS11-12 marine group (Bacteroidetes) contributed greatly to the stability of microbial co-occurrence in the Bay. Modularity and cluster structures of microbial networks varied spatiotemporally, which provided valuable insights into the 'small world' (a group of more interconnected species), network stability, and habitat partitioning/preferences.

CONCLUSION

Our results shed light on how estuarine gradients alter the spatiotemporal variations of prokaryotic microbial networks in the estuarine ecosystem, as well as their adaptability to environmental disturbances and co-occurrence network complexity and stability.

Spatiotemporal distribution of bacterial dimethylsulfoniopropionate producing and catabolic genes in the Changjiang Estuary

The osmolyte dimethylsulfoniopropionate (DMSP) is produced in petagram amounts by marine microorganisms. Estuaries provide natural gradients in salinity and nutrients, factors known to regulate DMSP production; yet there have been no molecular studies of DMSP production and cycling across these gradients. Here, we study the abundance, distribution and transcription of key DMSP synthesis (e.g. dsyB and mmtN) and catabolic (e.g. dddP and dmdA) genes along the salinity gradient of the Changjiang Estuary. DMSP levels did not correlate with Chl a across the salinity gradient. In contrast, DMSP concentration, abundance of bacterial DMSP producers and their dsyB and mmtN transcripts were lowest in the freshwater samples and increased abruptly with salinity in the transitional and seawater samples. Metagenomics analysis suggests bacterial DMSP-producers were more abundant than their algal equivalents and were more prominent in summer than winter samples. Bacterial DMSP catabolic genes and their transcripts followed the same trend of being greatly enhanced in transitional and seawater samples with higher DMSP levels than freshwater samples. DMSP cleavage was likely the dominant catabolic pathway, with DMSP lyase genes being ~4.3-fold more abundant than the demethylase gene dmdA. This is an exemplar study for future research on microbial DMSP cycling in estuary environments.

Disproportionate responses between free-living and particle-attached bacteria during the transition to oxygen-deficient zones in the Bohai Seawater

The Bohai Sea has recently suffered several seasonal oxygen-deficiency, even hypoxia events during the summer. To better understand effects of dissolved oxygen (DO) concentration on the bacterial composition in particle attached (PA) and free living (FL) fractions during the transition from oxic water to low oxygen conditions, the bacterial communities under three different oxygen levels, i.e., high oxygen (HO, close to 100% O₂ saturation), medium oxygen (MO, close to 75% O₂ saturation), and low oxygen (LO, close to 50% O₂ saturation) in the Bohai Sea were investigated using 16S rRNA amplicon sequencing. Fourteen water samples from 5 stations were collected during a cruise from August to September in 2018. The results showed that the sequences of Proteobacteria and Actinobacteriota jointly accounted for up to 74% across all 14 samples. The Shannon index in HO samples were significantly higher than in LO samples (P < 0.05), especially in PA communities. The composition of bacterial communities varied by oxygen concentration in all samples, and the effect was more pronounced in the PA fraction, which indicates that the PA fraction was more sensitive to the change in oxygen concentration, possibly due to the tighter interactions in this community than in the FL fraction. This study provides novel insights into the distribution of bacterial communities, and clues for understanding the responses of bacterial communities in the Bohai Sea during the transition from the oxic to oxygen-deficient zones.

Transformations from specialists to generalists cause bacterial communities are more stable than micro-eukaryotic communities under anthropogenic activity disturbance

Different microbial components have different responses to environmental disturbances. Here, we found that the planktonic bacterial and micro-eukaryotic communities had different responses to anthropogenic activity disturbance in a subtropical river, because they had different survival strategies (generalist and specialist). We used nutrients (nitrogen and phosphorus) as indicators of anthropogenic activities. We found that river stretch 1 showed low nutrient concentrations from October 2018 to September 2019. However, a nutrient disturbance was observed in river stretch 2. The nutrient concentrations increased largely in December and January but recovered to low values in June. Bacterial communities had higher resilience under this disturbance than micro-eukaryotic communities in river stretch 2. The bacterial community composition were quite different between the two river stretches in December and January but were similar in June and July. However, the differences of micro-eukaryotic community composition between the two river stretches were always high during the study period. The bacterial communities in river stretch 2 contained more generalists and nutrient tolerant specialists. The bacterial nutrient tolerant specialists rapidly decreased in the low nutrient months and were replaced by the generalists. Bacteria which were involved in this shifts accounted for 29.3% of the total abundance. However, the micro-eukaryotic communities in river stretch 2 contained more moderate generalists. These moderate generalists were insensitive to the variation of nutrients and only 19.56% of the micro-eukaryotes had significant responses to the disturbance. The survival strategies caused bacterial communities had higher adaptability than eukaryotes to environmental fluctuation.

Influence of hydrological factors on bacterial community structure in a tropical monsoonal estuary in India

In the present study, we analyzed variations in bacterial community structure along a salinity gradient in a tropical monsoonal estuary (Cochin estuary [CE]), on the southwest coast of India, using Illumina next-generation sequencing (NGS). Water samples were collected from eight different locations thrice a year to assess the variability in the bacterial community structure and to determine the physico-chemical factors influencing the bacterial diversity. Proteobacteria was the most dominant phyla in the estuary followed by Bacteroidetes, Cyanobacteria, Actinobacteria, and Firmicutes. Statistical analysis indicated significant variations in bacterial communities between freshwater and mesohaline and euryhaline regions, as well as between the monsoon (wet) and nonmonsoon (dry) periods. The abundance of Betaproteobacteria was higher in the freshwater regions, while Alphaproteobacteria and Epsilonproteobactera were more abundant in mesohaline and euryhaline regions of the estuary. Gammaproteobacteria was more abundant in regions with high nutrient concentrations. Various bacterial genera indicating the presence of fecal contamination and eutrophication were detected. Corrplot based on Pearson correlation analysis demonstrated the important physico-chemical variables (temperature, salinity, dissolved oxygen, and inorganic nutrients) that influence the distribution of dominant phyla, class, and genera. The observed spatio-temporal variations in bacterial community structure in the CE were governed by regional variations in anthropogenic inputs and seasonal variations in monsoonal rainfall and tidal influx.

Changes in protist communities in drainages across the Pearl River Delta under anthropogenic influence

Drainages in the Pearl River Delta urban agglomeration (PRDUA) host vital aquatic ecosystems and face enormous pressures from human activities in one of the largest urban agglomerations in the world. Despite being crucial components of aquatic ecosystems, the interactions and assembly processes of the protistan community are rarely explored in areas with serious anthropogenic disturbance. To elucidate the mechanisms of these processes, we used environmental DNA sequencing of 18S rDNA to investigate the influence of environmental factors and species interactions on the protistan community and its assembly in drainages of the PRDUA during summer. The protistan community showed a high level of diversity and a marked spatial pattern in this region. Community assembly was driven primarily by stochastic processes based on the Sloan neutral community model, explaining 74.28%, 75.82%, 73.67%, 74.40% and 51.24% of community variations in the BJ (Beijiang), XJ (Xijiang), PRD (Pearl River Delta), PRE (Pearl River Estuary) areas and in total, respectively. Meanwhile, environmental variables including temperature, pH, dissolved oxygen, transparency, nutrients and land use were strongly correlated with the composition and assembly of the protistan community, explaining 40.40% of variation in the protistan community. Furthermore, the bacterial community was simultaneously analysed by the 16S rDNA sequencing. Co-occurrence network analysis revealed that species interactions within bacteria (81.41% positive) or protists (82.80% positive), and those between bacteria and protists (50% positive and 50% negative) impacted the protistan community assembly. In summary, stochastic processes dominated, whereas species interactions and environmental factors also played important roles in shaping the protistan communities in drainages across the PRDUA. This study provides insights into the ecological patterns, assembly processes and species interactions underlying protistan dynamics in urban aquatic ecosystems experiencing serious anthropogenic disturbance.

Exploring Microbial Resource of Different Rhizocompartments of Dominant Plants Along the Salinity Gradient Around the Hypersaline Lake Ejinur

Lake littoral zones can also be regarded as another extremely hypersaline environment due to hypersaline properties of salt lakes. In this study, high-throughput sequencing technique was used to analyze bacteria and fungi from different rhizocompartments (rhizosphere and endosphere) of four dominant plants along the salinity gradient in the littoral zones of Ejinur Salt Lake. The study found that microbial α-diversity did not increase with the decrease of salinity, indicating that salinity was not the main factor on the effect of microbial diversity. Distance-based redundancy analysis and regression analysis were used to further reveal the relationship between microorganisms from different rhizocompartments and plant species and soil physicochemical properties. Bacteria and fungi in the rhizosphere and endosphere were the most significantly affected by SO₄ ^2-, SOC, HCO₃ ^-, and SOC, respectively. Correlation network analysis revealed the potential role of microorganisms in different root compartments on the regulation of salt stress through synergistic and antagonistic interactions. LEfSe analysis further indicated that dominant microbial taxa in different rhizocompartments had a positive response to plants, such as Marinobacter, Palleronia, Arthrobacter, and Penicillium. This study was of great significance and practical value for understanding salt environments around salt lakes to excavate the potential microbial resources.

Environmental filtering dominates bacterioplankton community assembly in a highly urbanized estuarine ecosystem

Estuaries are important in terms of biodiversity, biogeochemical function, and ecological balance due to their intense land-sea interactions. The sustainability of estuarine ecosystem function relies on a good understanding of the ecological processes related to microbial communities. However, microbial community assembly in such ecosystems is still not well understood. Here, based on 16S rRNA sequencing, we investigated the bacterioplankton community structure in the Pearl River Estuarine system during the wet and dry seasons. Results showed that there were significant seasonal and spatial variations in the bacterioplankton communities of the estuary, with seasonal variations being more remarkable. Multiple bacterioplankton with different abundances in the wet and dry seasons were observed, e.g., the class Actinobacteria and Oxyphotobacteria were enriched in the wet season, whereas Alphaproteobacteria and Saccharimonadia were more abundant in the dry season. Both variation partitioning and null model analysis revealed that environmental filtering dominated the bacterioplankton community assembly in the Pearl River Estuary. Water physical properties (e.g., salinity and temperature), nutrient content (e.g., nitrate), and upstream land use (e.g., urban land cover) together determined the distribution of the bacterioplankton composition in this highly urbanized estuarine ecosystem. These findings would help improve our understanding of the bacterioplankton communities in estuarine ecosystems and provide a theoretical foundation for estuarine ecological health management.

Characteristics of bacterial community structure and function associated with nutrients and heavy metals in coastal aquaculture area

Coastal aquaculture area has become one of the critical zones that are more susceptible to the influence of human activity. Many aquaculture operations invariably result in the accumulation of nutrients and heavy metals in the coastal ecosystem. Our study investigated sediment bacterial community structure and function across 23 sites under the influence of nutrients and heavy metals in the coastal aquaculture area. The habitat environment of the sediment was described by analyzing physicochemical characteristics. Sediment bacterial community structure and diversity were investigated by 16S rRNA sequencing. The sequencing data presented that Proteobacteria, Bacteroidetes, Planctomycetes, Acidobacteria and Chloroflexi were predominant at phylum level. Variations in the bacterial community composition and diversity were significant (P < 0.01) among different groups (according to the distance from the bank side) which indicated that specific environmental conditions had shaped distinct bacterial community. Specifically, bacterial diversity and composition were significantly influenced by the temperature, salinity, pH, dissolved oxygen (DO), TOC, TON, nitrite, nitrate and heavy metals (P < 0.05). Results related to functional prediction demonstrated that carbon, nitrogen and sulfur metabolism were the dominant processes in the coastal aquaculture area. In the meantime, the potential pathogens such as Arcobacter was found in site S3, which indicated the possible threat to the cultured species in this area. Overall, variations in bacterial communities caused by nutrients and heavy metals can affect biogeochemical cycles, which may provide an indication for the protection of coastal aquaculture environments.

Assembly processes and source tracking of planktonic and benthic bacterial communities in the Yellow River estuary

Estuaries connect rivers with the ocean and are considered transition regions due to the continuous inputs from rivers. Microbiota from different sources converge and undergo succession in these transition regions, but their assembly mechanisms along environmental gradients remain unclear. Here, we found that salinity had a stronger effect on planktonic than on benthic microbial communities, and the dominant planktonic bacteria changed more distinctly than the dominant benthic bacteria with changes in salinity. The planktonic bacteria in the brackish water came mainly from seawater, which was confirmed in the laboratory, whereas the benthic bacteria were weakly affected by salinity, which appeared to be a mixture of the bacteria from riverine and oceanic sediments. Benthic bacterial community assembly in the sediments was mainly controlled by homogeneous selection and almost unaffected by changes in salinity, the dominant assemblage processes for planktonic bacteria changed dramatically along the salinity gradient, from homogeneous selection in freshwater to drift in seawater. Our results highlight that salinity is the key driver of estuarine microbial succession and that salinity is more important in shaping planktonic than benthic bacterial communities in the Yellow River estuary.

In-depth Spatiotemporal Characterization of Planktonic Archaeal and Bacterial Communities in North and South San Francisco Bay

Despite being the largest estuary on the west coast of North America, no in-depth survey of microbial communities in San Francisco Bay (SFB) waters currently exists. In this study, we analyze bacterioplankton and archaeoplankton communities at several taxonomic levels and spatial extents (i.e., North versus South Bay) to reveal patterns in alpha and beta diversity. We assess communities using high-throughput sequencing of the 16S rRNA gene in 177 water column samples collected along a 150-km transect over a 2-year monthly time-series. In North Bay, the microbial community is strongly structured by spatial salinity changes while in South Bay seasonal variations dominate community dynamics. Along the steep salinity gradient in North Bay, we find that operational taxonomic units (OTUs; 97% identity) have higher site specificity than at coarser taxonomic levels and turnover ("species" replacement) is high, revealing a distinct brackish community (in oligo-, meso-, and polyhaline samples) from fresh and marine end-members. At coarser taxonomic levels (e.g., phylum, class), taxa are broadly distributed across salinity zones (i.e., present/abundant in a large number of samples) and brackish communities appear to be a mix of fresh and marine communities. We also observe variations in brackish communities between samples with similar salinities, likely related to differences in water residence times between North and South Bay. Throughout SFB, suspended particulate matter is positively correlated with richness and influences changes in beta diversity. Within several abundant groups, including the SAR11 clade (comprising up to 30% of reads in a sample), OTUs appear to be specialized to a specific salinity range. Some other organisms also showed pronounced seasonal abundance, including Synechococcus, Ca. Actinomarina, and Nitrosopumilus-like OTUs. Overall, this study represents the first in-depth spatiotemporal survey of SFB microbial communities and provides insight into how planktonic microorganisms have specialized to different niches along the salinity gradient.

Spatial variation in bacterial biomass, community composition and driving factors across a eutrophic river

Eutrophication is a global problem, and bacterial diversity and community composition are usually affected by eutrophication. However, limited information on the ecological significance of bacterial community during algae blooms of rivers has been given, more studies should be focused on the bacterial diversity and distribution characteristics in eutrophic rivers. In this study, we explored the spatial variations of bacterial biomass, community structure, and their relationship with environmental factors in the eutrophic Xiangxi River. The content of Chlorophyll (Chl) was about 16 mg/L in the midstream (S2, S3), which was in the range of light eutrophication. Significant spatial variation of bacterial community structure was found at different sites and depths (p < 0.05), and the driving environmental factor was found to be nitrogen, mainly detected as total nitrogen (TN), Kjeldahl nitrogen (KN), and ammonia nitrogen (NH₄⁺) (p < 0.05). The midstream sites had some significantly different bacteria, including algicidal bacteria and dominant lineages during algal blooms. This result was consistent with the functional prediction, where significant higher abundance of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways was associated with algicidal substances in the midstream. At different water depths, some populations adapted to the surface layer, such as the class Flavobacteriia, and others preferred to inhabit in the bottom layer, such as Betaproteobacteria and Acidobacteria. The bacterial biomass was higher in the bottom layer than that in the surface and middle layer, and temperature and pH were found to be the major driving factors. The bacterial diversity increased with the increasing of depths in most sampling sites according to operational taxonomic units (OTUs), Chao1 and ACE indexes, and PO₄^3- was demonstrated to be the most significant factor. In summary, this study offered the evidence for microbial distribution characteristics across different sites and depths in summer, and its relationship with environmental variables in a eutrophic river.

Shifts in methanogenic archaea communities and methane dynamics along a subtropical estuarine land use gradient

In coastal aquatic ecosystems, prokaryotic communities play an important role in regulating the cycling of nutrients and greenhouse gases. In the coastal zone, estuaries are complex and delicately balanced systems containing a multitude of specific ecological niches for resident microbes. Anthropogenic influences (i.e. urban, industrial and agricultural land uses) along the estuarine continuum can invoke physical and biochemical changes that impact these niches. In this study, we investigate the relative abundance of methanogenic archaea and other prokaryotic communities, distributed along a land use gradient in the subtropical Burnett River Estuary, situated within the Great Barrier Reef catchment, Australia. Microbiological assemblages were compared to physicochemical, nutrient and greenhouse gas distributions in both pore and surface water. Pore water samples from within the most urbanised site showed a high relative abundance of methanogenic Euryarchaeota (7.8% of all detected prokaryotes), which coincided with elevated methane concentrations in the water column, ranging from 0.51 to 0.68 μM at the urban and sewage treatment plant (STP) sites, respectively. These sites also featured elevated dissolved organic carbon (DOC) concentrations (0.66 to 1.16 mM), potentially fuelling methanogenesis. At the upstream freshwater site, both methane and DOC concentrations were considerably higher (2.68 μM and 1.8 mM respectively) than at the estuarine sites (0.02 to 0.66 μM and 0.39 to 1.16 mM respectively) and corresponded to the highest relative abundance of methanotrophic bacteria. The proportion of sulfate reducing bacteria in the prokaryotic community was elevated within the urban and STP sites (relative abundances of 8.0%– 10.5%), consistent with electron acceptors with higher redox potentials (e.g. O₂, NO₃^-) being scarce. Overall, this study showed that ecological niches in anthropogenically altered environments appear to give an advantage to specialized prokaryotes invoking a potential change in the thermodynamic landscape of the ecosystem and in turn facilitating the generation of methane–a potent greenhouse gas.

Seasonality in Spatial Turnover of Bacterioplankton Along an Ecological Gradient in the East China Sea: Biogeographic Patterns, Processes and Drivers

Seasonal succession in bacterioplankton is a common process in marine waters. However, seasonality in their spatial turnover is largely unknown. Here, we investigated spatial turnover of surface bacterioplankton along a nearshore-to-offshore gradient in the East China Sea across four seasons. Although seasonality overwhelmed spatial variability of bacterioplankton composition, we found significant spatial turnover of bacterioplankton along the gradient as well as overall seasonal consistency in biogeographic patterns (including distance-decay relationship and covariation of community composition with distance to shore) with subtle changes. Bacterioplankton assembly was consistently dominated by deterministic mechanisms across seasons, with changes in specific processes. We found overall seasonal consistency in abiotic factors (mainly salinity and nitrogen and phosphorus nutrients) shaping bacterioplankton composition, while phytoplankton showed a similar influence as abiotic factors only in spring. Although key taxa responsible for bacterioplankton spatial turnover showed certain season-specificity, seasonal switching between closely related taxa occurred within most dominant families. Moreover, many close relatives showed different responding patterns to the environmental gradients in different seasons, suggesting their differences in both seasonally climatic and spatially environmental preferences. Our results provide insights into seasonal consistency and variability in spatial turnover of bacterioplankton in terms of biogeographic patterns, ecological processes, and external and internal drivers.

Soil metabolome correlates with bacterial diversity and co-occurrence patterns in root-associated soils on the Tibetan Plateau

Metabolites in root-zone soils mediate microbe-to-microbe interactions and govern the overall microbial community. However, how chemicals relate to diversity and co-occurrence patterns of bacterial communities in root-associated soils is still poorly understood. Here, we studied the relationships of soil metabolome with bacterial community diversity and co-occurrence patterns in root-associated soils across different land types on the Tibetan Plateau. The soil metabolome mainly encompassed a range of organic acids, and sugars and sugar derivatives, which were widely negatively correlated with bacterial alpha-diversity. Compared to the investigated environmental variables, metabolites accounted more for the variations in the Shannon diversity and bacterial community compositions. Compared to sugars, organic acids accounted more for bacterial community compositions at high taxonomic ranks, while reversed at genus and species levels. The relative abundances of some bacterial genera and metabolites were closely linked to soil types and plant genotypes. The differential compounds were significantly correlated with the distinctive bacterial taxa across land types and plant genotypes. Keystone species in co-occurrence network, such as Bradyrhizobium, Bryobacter, and Microvirga were significantly correlated with sugars and organic acids. Structural equation modeling revealed that sugar metabolism can play a crucial role in altering the bacterial community diversity. This study provides new insights into the ecological mechanism that maintains bacterial community in the root-associated soils on the Tibetan Plateau.

Dredging mitigates cyanobacterial bloom in eutrophic Lake Nanhu: Shifts in associations between the bacterioplankton community and sediment biogeochemistry

Cyanobacterial blooms are a worldwide environmental problem, which is partly attributed to their access to excessive nitrogen (N) and phosphorus (P). Preventing the blooms by reducing N and P from internal inputs is viewed as a challenge. To evaluate the effects of dredging on cyanobacterial abundances and bacterioplankton communities, water and sediment samples were collected from eutrophic Lake Nanhu (Wuhan, China) before dredging (2017) and after dredging (2018). After dredging, significant decreases were observed for sediment nutrients (e.g., C, N, and P sources); C-, N-, P-, and S-cycling-related enzyme activity; N- and P-cycling-related gene abundance; microbial abundance; and dramatic changes were observed in the composition of the sediment microbial community. The release rates of nutrient including nitrogen, phosphorus, and organic matter decreased after dredging, and sediment biogeochemistry was closely correlated to nutrient release rates. Additionally, our observations and analyses indicated that the abundance and diversity of the bacterioplankton community decreased significantly, the composition and interaction of the bacterioplankton community dramatically changed, and the bacterioplankton community function (e.g., N, P-cycling-related enzymes and proteins) down regulated after dredging. Water and sediment physicochemical factors explained 72.28% variation in bacterioplankton community composition, and these physicochemical factors were significantly correlated with diversity, composition, and function of bacterioplankton community. Our findings emphasized that cyanobacterial blooms in freshwater ecosystems were closely correlated with noncyanobacterial bacterioplankton that were largely conserved at the phylum level, with Proteobacteria, Actinobacteria, and Bacteroidetes as the main taxa. To our knowledge, this is the first report clarifying the mechanism of cyanobacterial blooms mitigation by dredging, via changing the association between the bacterioplankton community and sediment biogeochemistry. Our findings are of significance and indicate that dredging is effective for mitigating cyanobacterial blooms.

DMSP-Producing Bacteria Are More Abundant in the Surface Microlayer than Subsurface Seawater of the East China Sea

Microbial production and catabolism of dimethylsulfoniopropionate (DMSP), generating the climatically active gases dimethyl sulfide (DMS) and methanethiol (MeSH), have key roles in global carbon and sulfur cycling, chemotaxis, and atmospheric chemistry. Microorganisms in the sea surface microlayer (SML), the interface between seawater and atmosphere, likely play an important role in the generation of DMS and MeSH and their exchange to the atmosphere, but little is known about these SML microorganisms. Here, we investigated the differences between bacterial community structure and the distribution and transcription profiles of the key bacterial DMSP synthesis (dsyB and mmtN) and catabolic (dmdA and dddP) genes in East China Sea SML and subsurface seawater (SSW) samples. Per equivalent volume, bacteria were far more abundant (~ 7.5-fold) in SML than SSW, as were those genera predicted to produce DMSP. Indeed, dsyB (~ 7-fold) and mmtN (~ 4-fold), robust reporters for bacterial DMSP production, were also far more abundant in SML than SSW. In addition, the SML had higher dsyB transcripts (~ 3-fold) than SSW samples, which may contribute to the significantly higher DMSP level observed in SML compared with SSW. Furthermore, the abundance of bacteria with dmdA and their transcription were higher in SML than SSW samples. Bacteria with dddP and transcripts were also prominent, but less than dmdA and presented at similar levels in both layers. These data indicate that the SML might be an important hotspot for bacterial DMSP production as well as generating the climatically active gases DMS and MeSH, a portion of which are likely transferred to the atmosphere.

Spatiotemporal dynamics of the total and active Vibrio spp. populations throughout the Changjiang estuary in China

Vibrio is ubiquitously distributed in marine environments and is the most extensively characterized group within Gammaproteobacteria. Studies have investigated Vibrio spp. worldwide, but mostly focused on pathogenic vibrios and based on cultivation methods. Here, using a combination of molecular and culturing methods, we investigated the dynamics of the total and active Vibrio spp. throughout the Changjiang estuary in China. The total Vibrio abundance was higher in summer (~6.59 × 10³ copies ml⁻¹) than in winter (~1.85 × 10³ copies ml⁻¹) and increased from freshwater to saltwater (e.g. 8.04 × 10¹ to 9.39 × 10³ copies ml⁻¹ in summer). The ratio of active to total Vibrio (Va/Vt) revealed a high activity of vibrios, with remarkable differences between freshwater and saltwater (p < 0.05). Based on the community compositions of the culturable, total and active Vibrio, Vibrio atlanticus and Vibrio owensii were the dominant and active species in winter and summer, respectively. The distribution of Vibrio was governed by the effects of diverse environmental factors, such as temperature, salinity, pH, dissolved oxygen and SiO₃²⁻. Our study clearly demonstrates the spatiotemporal dynamics of total and active Vibrio spp. and lays a foundation for fully understanding the ecological roles of marine Vibrio.

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.

Changes in biofilm bacterial communities in response to combined effects of hypoxia, ocean acidification and nutrients from aquaculture activity in Three Fathoms Cove

Anthropogenic nutrient enrichment results in hypoxia, ocean acidification and elevated nutrients (HOAN) in coastal environments throughout the world. Here, we examined the composition of biofilm bacterial communities from a nutrient-excessive fish farm with low dissolved oxygen (DO) and pH levels using 16S rRNA gene sequencing. HOAN was accompanied by higher bacterial diversity and richness, and resulted in an altered community composition than the control site. HOAN resulted in more Flavobacteriales, Rhizobiales, Epsilonproteobacteria and Vibrionales, but less Oceanospirillales and Alteromonadales. Photobacterium sp. and Vibrio sp. were mostly found to be exclusive to HOAN conditions, suggesting that HOAN could possibly proliferate the presence of these potential pathogens. Our study suggests the complexity of bacterial communities to hypoxia and acidification in response to increased nutrient loads, along with identities of nutrient, oxygen and pH-susceptible bacterial groups that are most likely affected under this ocean trend.

Microbial community composition across a coastal hydrological system affected by submarine groundwater discharge (SGD)

Mobile Bay, the fourth largest estuary in the USA located in the northern Gulf of Mexico, is known for extreme hypoxia in the water column during dry season caused by NH4+-rich and anoxic submarine groundwater discharge (SGD). Nutrient dynamics in the coastal ecosystem point to potentially elevated microbial activities; however, little is known about microbial community composition and their functional roles in this area. In this study, we investigated microbial community composition, distribution, and metabolic prediction along the coastal hydrological compartment of Mobile Bay using 16S rRNA gene sequencing. We collected microbial samples from surface (river and bay water) and subsurface water (groundwater and coastal pore water from two SGD sites with peat and sandy lithology, respectively). Salinity was identified as the primary factor affecting the distribution of microbial communities across surface water samples, while DON and PO43- were the major predictor of community shift within subsurface water samples. Higher microbial diversity was found in coastal pore water in comparison to surface water samples. Gammaproteobacteria, Bacteroidia, and Oxyphotobacteria dominated the bacterial community. Among the archaea, methanogens were prevalent in the peat-dominated SGD site, while the sandy SGD site was characterized by a higher proportion of ammonia-oxidizing archaea. Cyanobium PCC-6307 and unclassified Thermodesulfovibrionia were identified as dominant taxa strongly associated with trends in environmental parameters in surface and subsurface samples, respectively. Microbial communities found in the groundwater and peat layer consisted of taxa known for denitrification and dissimilatory nitrate reduction to ammonium (DNRA). This finding suggested that microbial communities might also play a significant role in mediating nitrogen transformation in the SGD flow path and in affecting the chemical composition of SGD discharging to the water column. Given the ecological importance of microorganisms, further studies at higher taxonomic and functional resolution are needed to accurately predict chemical biotransformation processes along the coastal hydrological continuum, which influence water quality and environmental condition in Mobile Bay.

Spatial Variation in Bacterioplankton Communities in the Pearl River, South China: Impacts of Land Use and Physicochemical Factors

River ecosystems are critical for human and environmental health, with bacterioplankton playing a vital role in biogeochemical cycles. Unveiling the spatial patterns of bacterioplankton communities in relation to environmental factors is important for understanding the processes of microbial variation and functional maintenance. However, our understanding of the correlations among bacterioplankton communities, physicochemical factors, and land use, especially in large rivers affected by intensive anthropogenic activities, remains relatively poor. Here, we investigated the bacterioplankton communities in July 2018 in three main tributaries of the Pearl River, i.e., Beijiang, Xijiang, and Pearl River Delta, based on 16S rRNA high-throughput sequencing. Results showed that the most dominant phyla, Proteobacteria, Actinobacteria, Cyanobacteria, and Planctomycetes accounted for 33.75%, 22.15%, 11.65%, and 10.48% of the total abundance, respectively. The bacterioplankton communities showed remarkable differences among the three tributaries in terms of composition, structure, diversity, and predictive functional profiles. Mantel and partial Mantel tests revealed that the bacterioplankton communities were affected by physicochemical variables (p < 0.01) and land use (p < 0.01). Redundancy analysis identified specific conductivity, dissolved oxygen, agricultural land, ammonium, urban land, and water transparency as the dominant environmental factors influencing the bacterioplankton communities in the Pearl River. Variation partitioning analysis indicated that both physicochemical factors and land use had direct effects on the bacterioplankton community, and that land use may also shape bacterioplankton communities through indirect effects of physicochemical factors on riverine ecosystems. This study provides fundamental information on the diversity, spatial patterns, and influencing factors of bacterioplankton communities in the Pearl River, which should enhance our understanding of how such communities change in response to environmental gradients and anthropogenic activities.

Niche Differentiation of Host-Associated Pelagic Microbes and Their Potential Contribution to Biogeochemical Cycling in Artificially Warmed Lakes

It has been proposed that zooplankton-associated microbes provide numerous beneficial services to their "host". However, there is still a lack of understanding concerning the effect of temperature on the zooplankton microbiome. Furthermore, it is unclear to what extent the zooplankton microbiome differs from free-living and particle-associated (PA) microbes. Here, we explicitly addressed these issues by investigating (1) the differences in free-living, PA, and zooplankton associated microbes and (2) the impact of temperature on these microbes in the water column of a series of lakes artificially warmed by two power plants. High-throughput amplicon sequencing of the 16S rRNA gene showed that diversity and composition of the bacterial community associated to zooplankton, PA, and bacterioplankton varied significantly from one another, grouping in different clusters indicating niche differentiation of pelagic microbes. From the abiotic parameters measured, temperature significantly affected the diversity and composition of all analyzed microbiomes. Two phyla (e.g., Proteobacteria and Bacteroidetes) dominated in zooplankton microbiomes whereas Actinobacteria was the dominant phylum in the bacterioplankton. The microbial species richness and diversity was lower in zooplankton compared to bacterioplankton and PA. Surprisingly, genera of methane-oxidizing bacteria, methylotrophs and nitrifiers (e.g., Nitrobacter) significantly associated with the microbiome of zooplankton and PA. Our study clearly demonstrates niche differentiation of pelagic microbes and their potential link to biogeochemical cycling in freshwater systems.