Distinct Seasonal Patterns of Bacterioplankton Abundance and Dominance of Phyla α-Proteobacteria and Cyanobacteria in Qinhuangdao Coastal Waters Off the Bohai Sea

Phylogenetic diversity and functional potential of large and cell-associated viruses in the Bay of Bengal

IMPORTANCE

The BoB, the world's largest bay, is of significant economic importance to surrounding countries, particularly Bangladesh, which heavily relies on its coastal resources. Concurrently, the BoB holds substantial ecological relevance due to the region's high vulnerability to climate change-induced impacts. Yet, our understanding of the BoB's microbiome in relation to marine food web and biogeochemical cycling remains limited. Particularly, there are little or no data on the viral diversity and host association in the BoB. We examined the viral community in two distinct BoB coastal regions to reveal a multitude of viral species interacting with a wide range of microbial hosts, some of which play key roles in coastal biogeochemical cycling or potential pathogens. Furthermore, we demonstrate that the BoB coast harbors a diverse community of large and giant viruses, underscoring the importance of investigating understudied environments to discover novel viral lineages with complex metabolic capacities.

Unveiling the Microbiome Landscape: A Metagenomic Study of Bacterial Diversity, Antibiotic Resistance, and Virulence Factors in the Sediments of the River Ganga, India

The global rise in antibiotic resistance, fueled by indiscriminate antibiotic usage in medicine, aquaculture, agriculture, and the food industry, presents a significant public health challenge. Urban wastewater and sewage treatment plants have become key sources of antibiotic resistance proliferation. The present study focuses on the river Ganges in India, which is heavily impacted by human activities and serves as a potential hotspot for the spread of antibiotic resistance. We conducted a metagenomic analysis of sediment samples from six distinct locations along the river to assess the prevalence and diversity of antibiotic resistance genes (ARGs) within the microbial ecosystem. The metagenomic analysis revealed the predominance of Proteobacteria across regions of the river Ganges. The antimicrobial resistance (AMR) genes and virulence factors were determined by various databases. In addition to this, KEGG and COG analysis revealed important pathways related to AMR. The outcomes highlight noticeable regional differences in the prevalence of AMR genes. The findings suggest that enhancing health and sanitation infrastructure could play a crucial role in mitigating the global impact of AMR. This research contributes vital insights into the environmental aspects of antibiotic resistance, highlighting the importance of targeted public health interventions in the fight against AMR.

Effects of Environmental and Water Quality Variables on Histamine-Producing Bacteria Concentration and Species in the Northern Gulf of Mexico

Scombrotoxin (histamine) fish poisoning is a common seafood-borne illness attributed to toxin production by histamine-producing bacteria (HPB) in fish tissues during decomposition. In laboratory studies, growth of HPB and other bacterial species is affected by physical and chemical attributes, but natural communities of HPB are not well understood. To determine how in situ environmental and water quality variables may affect density of HPB in the natural aquatic environment, we compared presence and abundance of HPB to ambient temperature, salinity, dissolved oxygen, fecal coliforms, male-specific coliphage, nutrient concentrations, carbon and nitrogen stable isotope ratios, and C:N in water samples collected from July 2017 to February 2018 along a natural salinity gradient in a tidal river on the coast of northern Gulf of Mexico. HPB in water samples were quantified using a real-time PCR, most probable number method. HPB species were identified via 16S rRNA gene sequences. Temperature and salinity were determined to be the main factors driving HPB presence and concentration. Canonical correspondence analysis revealed that different HPB were associated with different environmental conditions. Photobacterium damselae was found under warmer, higher-salinity conditions; Raoultella planticola was found at colder, lower-salinity conditions; Enterobacter aerogenes was found at warmer, lower-salinity conditions; and Morganella morganii was found at most sites, independent of environmental conditions. These results showed that naturally occurring HPB abundance and species composition can be affected by environmental conditions, which could manifest in various potentials for histamine formation and scombrotoxin fish poisoning risk based on environmental factors. IMPORTANCE This study determined the effects of environmental conditions on presence and abundance of naturally occurring histamine-producing bacteria in the northern Gulf of Mexico. Here, we show that HPB abundance and species composition are related to in situ ambient temperature and salinity, with the magnitude of this effect dependent on the particular HPB species. This finding suggests that environmental conditions at fishing sites could affect the risk of human illness from scombrotoxin (histamine) fish poisoning.

Bacterial taxonomic and functional profiles from Bohai Sea to northern Yellow Sea

Microbial distribution patterns are the result of a combination of biotic and abiotic factors, which are the core issues in microbial ecology research. To better understand the biogeographic pattern of bacteria in water environments from the Bohai Sea to the northern Yellow Sea, the effects of environmental factors, and spatial distance on the structure of bacterial communities in marine water were investigated using high-throughput sequencing technology based on 16S rRNA genes. The results showed that Proteobacteria, Bacteroidetes, Actinobacteri, Desulfobacterota, and Bdellovibrionota were the dominant phyla in the study area. A clear spatial pattern in the bacterial community was observed, and environmental factors, including salinity, nutrient concentration, carbon content, total phosphorus, dissolved oxygen, and seawater turbidity emerged as the central environmental factors regulating the variation in bacterial communities. In addition, the study provides direct evidence of the existence of dispersal limitation in this strongly connected marine ecological system. Therefore, these results revealed that the variation in bacterial community characteristics was attributed to environmental selection, accompanied by the regulation of stochastic diffusion. The network analysis demonstrated a nonrandom co-occurrence pattern in the microbial communities with distinct spatial distribution characteristics. It is implied that the biogeography patterns of bacterial community may also be associated with the characteristics of co-occurrence characterize among bacterial species. Furthermore, the PICRUSt analysis indicated a clear spatial distribution of functional characteristics in bacterial communities. This functional variation was significantly modulated by the environmental characteristics of seawater but uncoupled from the taxonomic characteristics of bacterial communities (e.g., diversity characteristics, community structure, and co-occurrence relationships). Together, this findings represent a significant advance in linking seawater to the mechanisms underlying bacterial biogeographic patterns and community assembly, co-occurrence patterns, and ecological functions, providing new insights for identifying the microbial ecology as well as the biogeochemical cycle in the marine environment.

Heterogeneous selection dominated the temporal variation of the planktonic prokaryotic community during different seasons in the coastal waters of Bohai Bay

To explore temporal and spatial effects on the planktonic prokaryotic community composition (PCC) in the coastal region of the Bohai Sea, surface water samples were collected from 12  to  28 regularly distributed sites in Bohai Bay across 3 months from different seasons to characterize the PCC using high-throughput sequencing of the 16S rRNA V4 region. Prokaryotic α- and β-diversity showed significant temporal variation during the three sampling months. VPA analysis based on both weighted and unweighted UniFrac distances exhibited a shift of environmental and spatial effects on PCC variation with temporal variation. Quantification analysis of assembly processes on community turn over showed that "heterogeneous selection" dominated for PCC temporal variation, with basic abiotic parameters such as temperature, pH, ammonia nitrogen as the driving factors. Analysis of seasonal features showed that seasonal specific OTUs (ssOTUs) exhibited different seasonal attributions under the same phylum; meanwhile, the ssOTUs showed significant correlations with the driving environmental factors, which suggested that finer-level analysis was needed to more strictly reflect the temporal variation. Moreover, predicted nitrogen and sulfur metabolism were significantly shifted during the temporal variation. Our results clearly showed that seasonally varied environmental factors drive the "heterogeneous selection" process for PCC assembly in seawaters of Bohai Bay during different sampling seasons.

Determinism governs the succession of disturbed bacterioplankton communities in a coastal maricultural ecosystem

Bacterioplankton community is the major engine that drives the biogeochemical cycling of various nutrient and essential elements in the coastal ecosystem. Unraveling the mechanisms governing the succession of such complex bacterioplankton communities in dynamic environment is a challenging issue in environmental science. In this study, we investigated the diversity patterns and succession mechanisms of both free-living and particle-attached bacterioplankton communities that have been exposed to low oxygen and typhoon Lekima. The community evenness was the lowest in August when the temperature was high and dissolved oxygen was low. Similar patterns in community succession were observed for free-living and particle-attached bacterioplankton community after the passing through of typhoon Lekima. Both the free-living and particle-attached bacterioplankton communities in the surface and bottom water columns were strongly affected by geo-environmental factors, among which temperature was the common factor, suggesting that the metabolic theory of ecology also underlie the dynamic patterns of bacterioplankton communities. Although the surface and bottom bacterioplankton compositions were initially different taxonomically and shaped by different environmental conditions, they followed a similar succession pattern over the sampling months. Temperature, dissolved inorganic carbon and dissolved inorganic phosphorus were the major factors associated with the variations of surface bacterioplankton ASVs. Time-decay relationship, in which community similarity decreases with increasing time interval, was clearly observed. Such pattern shall be attributed to the combined effects of time and the changing environmental factors over the sampling months, rather than time alone. Integrating multiple lines of evidences, we demonstrated that determinism governed the succession of both free-living and particle-attached bacterioplankton communities in the coastal maricultural ecosystem, with higher stochastic ratio in habitable months (i.e. fall). This study is expected to provide valuable mechanistic insights into the succession of disturbed complex bacterioplankton communities.

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.

Patchy Blooms and Multifarious Ecotypes of Labyrinthulomycetes Protists and Their Implication in Vertical Carbon Export in the Pelagic Eastern Indian Ocean

Labyrinthulomycetes protists are an important heterotrophic component of microeukaryotes in the world’s oceans, but their distribution patterns and ecological roles are poorly understood in pelagic waters. This study employed flow cytometry and high-throughput sequencing to characterize the abundance, diversity, and community structure of Labyrinthulomycetes in the pelagic Eastern Indian Ocean. The total Labyrinthulomycetes abundance varied much more among stations than did the abundance of prokaryotic plankton, reaching over 1,000 cells mL⁻¹ at a few “bloom” stations. The total Labyrinthulomycetes abundance did not decline with depth throughout the whole water column (5 to 2,000 m) like the abundance of prokaryotic plankton did, and the Labyrinthulomycetes average projected biomass over all samples was higher than that of the prokaryotic plankton. However, Labyrinthulomycetes diversity showed obvious vertical variations, with richness, Shannon diversity, and evenness greatest in the upper epipelagic, lower epipelagic, and deep waters, respectively. Many abundant phylotypes were detected across multiple water layers, which aligned with the constant vertical Labyrinthulomycetes biomass, suggesting potential sinking and contribution to the biological pump. Hierarchical clustering revealed distinct ecotypes partitioning by vertical distribution patterns, suggesting their differential roles in the carbon cycle and storage processes. Particularly, most phylotypes showed patchy distributions (occurring in only few samples) as previously found in the coastal waters, but they were less associated with the Labyrinthulomycetes blooms than the prevalent phylotypes. Overall, this study revealed distinct patterns of Labyrinthulomycetes ecotypes and shed light on their importance in the pelagic ocean carbon cycling and sequestration relative to that of the prokaryotic plankton.

IMPORTANCE While prokaryotic heterotrophic plankton are well accepted as major players in oceanic carbon cycling, the ecological distributions and functions of their microeukaryotic counterparts in the pelagic ocean remain largely unknown. This study focused on an important group of heterotrophic (mainly osmotrophic) protistan microbes, the Labyrinthulomycetes, whose biomass can surpass that of the prokaryotic plankton in many marine ecosystems, including the bathypelagic ocean. We found patchy horizontal but persistent vertical abundance profiles of the Labyrinthulomycetes protists in the pelagic waters of the Eastern Indian Ocean, which were distinct from the spatial patterns of the prokaryotic plankton. Moreover, multiple Labyrinthulomycetes ecotypes with distinct vertical patterns were detected and, based on the physiologic, metabolic, and genomic understanding of their cultivated relatives, were inferred to play multifaceted key roles in the carbon cycle and sequestration, particularly as contributors to the vertical carbon export from the surface to the dark ocean, i.e., the biological pump.

High-Frequency Variability of Bacterioplankton in Response to Environmental Drivers in Red Sea Coastal Waters

Autotrophic and heterotrophic bacterioplankton are essential to the biogeochemistry of tropical ecosystems. However, the processes that govern their dynamics are not well known. We provide here a high-frequency assessment of bacterial community dynamics and concurrent environmental factors in Red Sea coastal waters. Weekly sampling of surface samples during a full annual cycle at an enclosed station revealed high variability in ecological conditions, which reflected in changes of major bacterioplankton communities. Temperature varied between 23 and 34°C during the sampling period. Autotrophic (Synechococcus, 1.7–16.2 × 10⁴ cells mL⁻¹) and heterotrophic bacteria (1.6–4.3 × 10⁵ cells mL⁻¹) showed two maxima in abundance in spring and summer, while minima were found in winter and autumn. Heterotrophic cells with high nucleic acid content (HNA) peaked in July, but their contribution to the total cell counts (35–60%) did not show a clear seasonal pattern. Actively respiring cells (CTC+) contributed between 4 and 51% of the total number of heterotrophic bacteria, while live cells (with intact membrane) consistently accounted for over 90%. Sequenced 16S rRNA amplicons revealed a predominance of Proteobacteria in summer and autumn (>40%) and a smaller contribution in winter (21–24%), with members of the Alphaproteobacteria class dominating throughout the year. The contribution of the Flavobacteriaceae family was highest in winter (21%), while the Rhodobacteraceae contribution was lowest (6%). Temperature, chlorophyll-a, and dissolved organic carbon concentration were the environmental variables with the greatest effects on bacterial abundance and diversity patterns.

Inter-phylum negative interactions affect soil bacterial community dynamics and functions during soybean development under long-term nitrogen fertilization

Understanding interspecies interactions is essential to predict the response of microbial communities to exogenous perturbation. Herein, rhizospheric and bulk soils were collected from five developmental stages of soybean, which grew in soils receiving 16-year nitrogen inputs. Bacterial communities and functional profiles were examined using high-throughput sequencing and quantitative PCR, respectively. The objective of this study was to identify the key bacterial interactions that influenced community dynamics and functions. We found that the stages of soybean development outcompeted nitrogen fertilization management in shaping bacterial community structure, while fertilization treatments significantly shaped the abundance distribution of nitrogen functional genes. Temporal variations in bacterial abundances increased in bulk soils, especially at the stage of soybean branching, which helps to infer underlying negative interspecies interactions. Members of Cyanobacteria and Actinobacteria actively engaged in inter-phylum negative interactions in bulk soils and soybean rhizosphere, respectively. Furthermore, the negative interactions between nitrogen-fixing functional groups and the reduction of nifH gene abundance were coupled during soybean development, which may help to explain the linkages between population dynamics and functions. Overall, these findings highlight the importance of inter-phylum negative interactions in shaping the correlation patterns of bacterial communities and in determining soil functional potential.

Composition change and decreased diversity of microbial eukaryotes in the coastal upwelling waters of South China Sea

Upwelling plays an important role in marine ecosystems and potentially reshapes microbial communities by enhanced dispersal and distinct environmental drivers. Relative to that of bacterioplankton, however, the response of eukaryotic microbes to upwelling is largely unknown. Here, we investigated the influence of coastal upwelling in South China Sea on the microbial eukaryotic communities. Unlike several folds of increase in the cell abundance of bacterioplankton in upwelling than non-upwelling stations at corresponding water layers, no significant difference was detected for the total microbial eukaryotic 18S rRNA gene abundance. Moreover, the microbial eukaryotes in the upwelling stations exhibited increasing 18S rRNA gene abundance from the surface to the deep, contrasting the vertical cell abundance pattern of the bacterioplankton; but their vertical abundance patterns were similar in non-upwelling stations. Importantly, the coastal upwelling significantly reduced the community evenness of the microbial eukaryotes and slightly reduced their Shannon diversity. Their community composition also varied obviously especially between the surface waters of upwelling and non-upwelling stations. Among the dominant supergroups, Alveolata was found to be less abundant while Stramenopiles, particularly thraustochytrids and diatoms, to be more abundant in the surface water of upwelling than non-upwelling stations. Temperature was identified as the most important factor of the microbial eukaryotic community composition, suggesting potential effects of the cold upwelling water masses on specific taxa. Overall, our results reveal significant and distinct impacts of coastal upwelling on the abundance, diversity, and community structure of microbial eukaryotes, filling the knowledge gap about the microbial responses to this important marine phenomenon.

Disentangling the structure and function of mycoplankton communities in the context of marine environmental heterogeneity

Mycoplankton are a diverse and ubiquitous component of marine environments with a suggested role in ocean biogeochemical cycling. Thus far, the patterns of their abundance, structure, and function against spatial environmental heterogeneity remains poorly understood. Based on in silico and experimental evaluation of multiple markers, we adopted the ITS1 region to determine the composition, guilds, and metabolic potential of mycoplankton communities in contrasting marine environments. The trophic status of estuarine (SB1 and SB2) and coastal (DB1 and DB2) sites, but not oceanic (OS) site, was the major factor that determined their abundances. While ascomycetous fungi dominated the estuarine and coastal sites, basidiomycetous fungi were found to dominate the oceanic site. The zoosporic fungi were relatively more abundant in SB1 and DB2 sites compared to the other sites. The relative abundances of the core fungi, namely Cystobasidium, Phlebia, Rhodotorula, Trichoderma, Alternaria, Penicillium, Malassezia, and Aspergillus varied widely across the sites. Additionally, several fungal genera unique to each site were also identified. DB2 site exhibited the lowest fungal richness while the OS site the highest. Conversely, the diversity and evenness were the lowest for the OS site but highest for the SB1 site. Temperature, pH, and chlorophyll-a were strongly associated with spatial diversity patterns. Of the 11 assigned guilds, some guilds particularly were not detected, including plant pathogen-wood saprotroph in DB2, the endophyte-plant pathogen in OS, the animal pathogen in SB1, and fungal parasite in DB1 and SB2. Within core functions-metabolism of amino acids, carbohydrates and energy, fatty acids and lipids, nitrogen, sulfur, and other compounds-several pathways showed spatial variations. Overall, this study not just broadens the taxonomic and metabolic repertoire of marine mycoplankton but also provides the first evidence of how these are shaped by site-scale environmental heterogeneity.

Annual Partitioning Patterns of Labyrinthulomycetes Protists Reveal Their Multifaceted Role in Marine Microbial Food Webs

Heterotrophic microbes play a key role in remineralizing organic material in the coastal ocean. While there is a significant body of literature examining heterotrophic bacterioplankton and phytoplankton communities, much less is known about the diversity, dynamics, and ecology of eukaryotic heterotrophs. Here, we focus on the Labyrinthulomycetes, a fungus-like protistan group whose biomass can exceed that of the bacterioplankton in coastal waters. We examined their diversity and community structure in a weekly temperate coastal ocean time series. Their seasonal community patterns were related to temperature, insolation, dissolved inorganic carbon, fungal abundance, ammonia, chlorophyll a, pH, and other environmental variables. Similar to the bacterioplankton, annual community patterns of the Labyrinthulomycetes were dominated by a few persistent taxa with summer or winter preferences. However, like the patterns of fungi at this site, the majority of the Labyrinthulomycetes phylotypes occurred mostly as short, reoccurring, season-specific blooms. Furthermore, some specific phylotypes of Labyrinthulomycetes displayed time-lagged correlations or cooccurrences with bacterial, algal, or fungal phylotypes, suggesting their potentially multifaceted involvement in the marine food webs. Overall, this study reports niche partitioning between closely related Labyrinthulomycetes and identifies distinct ecotypes and temporal patterns compared to bacterioplankton and fungi.IMPORTANCE Increasing evidence has shown that heterotrophic microeukaryotes are an important component in global marine ecosystems, while their diversity and ecological functions remain largely unknown. Without appropriately incorporating these organisms into the food web models, our current understanding of marine microbial community ecology is incomplete, which may further hamper broader studies of biogeochemistry and climate change. This study focuses on a major group of unicellular fungus-like protists (Labyrinthulomycetes) and reveals their distinct annual community patterns relative to fungi and bacteria. Results of our observations provide new information on the community structure and ecology of this protistan group and shed light on the intricate ecological roles of unicellular heterotrophic eukaryotes in the coastal oceans.

Bacterial community composition and diversity in the ballast water of container ships arriving at Yangshan Port, Shanghai, China

Ballast water is a major vector of invasion by protozoans and metazoans. Bacterial invasion is less-well understood. We surveyed the bacterial diversity of ballast water from 26 container ships arriving at the Yangshan Deepwater Port, Shanghai, China during 2015-2016. We characterized the ballast microbiome using high-throughput sequencing (HTS) based on V4-V5 region of 16S rRNA genes. We simultaneously monitored physicochemical parameters of the ballast water, including temperature, pH, dissolved oxygen (DO), salinity, turbidity, total suspended solid (TSS), particulate organic carbon (POC), NO₂, NH₄, PO₄. Proteobacteria was the dominant phylum, comprising more than 50% of the OTUs of almost all vessels, followed by Bacteroidetes (12.08%), Actinobacteria (4.86%) Planctomycetes (3.24%) and Cyanobacteria (1.95%). The relative abundance of Cyanobacteria differed among vessels. It was negatively correlated with temperature, NO₃, pH, TSS, PO₄, and turbidity and positively correlated with NH₄, POC. The genus Synechococcus was the most common Cyanobacteria in our results. Escherichia coli were relatively rare; they are indicator-species of D-2 standards published by the IMO. The relative abundance of the genus Vibrio ranged from 0.003% to 24.88% among different vessels. Our results showed that HTS was able to profile the bacterial communities in ballast-waters, even when the approach was restricted by technical and other obstacles.

Assessing the water quality impacts of two Category-5 hurricanes on St. Thomas, Virgin Islands

Managing waterborne and water-related diseases is one of the most critical factors in the aftermath of hurricane-induced natural disasters. The goal of the study was to identify water-quality impairments in order to set the priorities for post-hurricane relief and to guide future decisions on disaster preparation and relief administration. Field investigations were carried out on St. Thomas, U.S. Virgin Islands as soon as the disaster area became accessible after the back-to-back hurricane strikes by Irma and Maria in 2017. Water samples were collected from individual household rain cisterns, the coastal ocean, and street-surface runoffs for microbial concentration. The microbial community structure and the occurrence of potential human pathogens were investigated in samples using next generation sequencing. Loop mediated isothermal amplification was employed to detect fecal indicator bacteria, Enterococcus faecalis. The results showed both fecal indicator bacteria and Legionella genetic markers were prevalent but were low in concentration in the water samples. Among the 22 cistern samples, 86% were positive for Legionella and 82% for Escherichia-Shigella. Enterococcus faecalis was detected in over 68% of the rain cisterns and in 60% of the coastal waters (n = 20). Microbial community composition in coastal water samples was significantly different from cistern water and runoff water. Although identification at bacterial genus level is not direct evidence of human pathogens, our results suggest cistern water quality needs more organized attention for protection of human health, and that preparation and prevention measures should be taken before natural disasters strike.

Bacterioplankton community variation in Bohai Bay (China) is explained by joint effects of environmental and spatial factors

Parsing the relative importance of environmental (recent disturbances) and spatial factors (historical processes) in determining community structure is a core issue in ecology. The Bohai Bay is a typical semi‐enclosed bay located in the north of China, surrounding by the metropolitan area with anthropogenic disturbances made it a complex marine coastal system with pollution gradients, where the distributions and determinants of bacterioplankton communities remain unclear. In this study, we collected surface water samples from 19 sites across Bohai Bay at about 100 km scale to investigate the relative roles of local environments and regional spatial factors in shaping bacterioplankton community composition (BCC). The environmental parameters in the sampling region showed gradient change according to the geographic variation. Several abundant OTUs were significantly correlated with the pollution parameters in the studied area, and 16 OTUs of them showed distinct distribution pattern in different polluted regions with obvious geographic segmentation, which indicated the effects of pollution gradient and dispersal limitation on specific taxon. The BCCs did not show obviously clustering effect between different polluted regions, which indicated the complexity for explaining the BCC variation in the studied region. The partial Mantel test revealed stronger spatial effects on beta diversity than those of local environmental factors, which indicated that dispersal limitation accounted more for the beta diversity than environmental heterogeneity. Furthermore, variation partitioning analysis (VPA) conducted by combining the environmental variables, linear trends, and principal coordinates of the variables from neighbor matrices (PCNM) showed that it was the joint effects of environmental and spatial factors contributed to the explained variation of BCC in the studied area. Considering the special human geography characteristics of Bohai Bay, the unmeasured biotic/abiotic factors, stochastic factors, and anthropogenic disturbances may be responsible for the unexplained variation of the BCC.

Airborne bacteria in the Central Mediterranean: Structure and role of meteorology and air mass transport

The 16S rRNA gene metabarcoding approach has been used to characterize the structure of the airborne bacterial community of PM10 samples, and investigate the dependence on meteorology, seasons, and long-range transported air masses. The PM10 samples were collected at a Central Mediterranean coastal site, away from large sources of local pollution. Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, and Bacteroidetes, which were found in all samples, were the most abundant phyla. Calothrix, Pseudomonas, and Bacillus were the most abundant genera. The within-sample relative abundance (RA) of each phylum/genus varied from sample to sample. Calothrix was the most abundant genus during the advection of desert dust and Atlantic air masses, Pseudomonas was the most abundant genus when the advected air flows spent several hours over lands or close to lands affected by anthropogenic activities, before reaching the study site. The bacterial community richness and biodiversity of the PM10 samples on average increased from winter to spring, while the sample dissimilarity on average decreased from winter to spring. The spring meteorological conditions over the Mediterranean, which have likely contributed to maintain for longer time the bacterial community in the atmosphere, could have been responsible for the above results. The analysis of the presumptive species-level characterization of the airborne bacterial community has revealed that the abundance of human (opportunistic) pathogens was highly inhomogeneous among samples, without any significant change from winter to spring. We also found that the PM10 samples collected during the advection of desert dust and Atlantic air masses were on average the less enriched in human (opportunistic) pathogenic species.

Archaeal community variation in the Qinhuangdao coastal aquaculture zone revealed by high-throughput sequencing

The differences in archaeal diversity and community composition in the sediments and waters of the Qinhuangdao coastal aquaculture zone were investigated. Furthermore, the associations between dominant archaeal taxa with geographic and environmental variables were evaluated. High-throughput sequencing of archaeal 16S rRNA genes yielded a total of 176,211 quality-filtered reads and 1,178 operational taxonomic units (OTUs) overall. The most abundant phylum and class among all communities were Thaumarchaeota and Nitrososphaeria, respectively. Beta diversity analysis indicated that community composition was divided into two groups according to the habitat type (i.e., sediments or waters). Only 9.8% OTUs were shared by communities from the two habitats, while 73.9% and 16.3% of the OTUs were unique to sediment or water communities, respectively. Furthermore, the relative abundances of the dominant OTUs differed with habitat type. Investigations of relationships between dominant OTUs and environmental variables indicated that some dominant OTUs were more sensitive to variation in environmental factors, which could be due to individual taxonomic differences in lifestyles and biological processes. Overall, the investigation of archaeal community variation within the Qinhuangdao coastal aquaculture zone provides an important baseline understanding of the microbial ecology in this important ecosystem.

Community ecology across bacteria, archaea and microbial eukaryotes in the sediment and seawater of coastal Puerto Nuevo, Baja California

Microbial communities control numerous biogeochemical processes critical for ecosystem function and health. Most analyses of coastal microbial communities focus on the characterization of bacteria present in either sediment or seawater, with fewer studies characterizing both sediment and seawater together at a given site, and even fewer studies including information about non-bacterial microbial communities. As a result, knowledge about the ecological patterns of microbial biodiversity across domains and habitats in coastal communities is limited-despite the fact that archaea, bacteria, and microbial eukaryotes are present and known to interact in coastal habitats. To better understand microbial biodiversity patterns in coastal ecosystems, we characterized sediment and seawater microbial communities for three sites along the coastline of Puerto Nuevo, Baja California, Mexico using both 16S and 18S rRNA gene amplicon sequencing. We found that sediment hosted approximately 500-fold more operational taxonomic units (OTUs) for bacteria, archaea, and microbial eukaryotes than seawater (p < 0.001). Distinct phyla were found in sediment versus seawater samples. Of the top ten most abundant classes, Cytophagia (bacterial) and Chromadorea (eukaryal) were specific to the sediment environment, whereas Cyanobacteria and Bacteroidia (bacterial) and Chlorophyceae (eukaryal) were specific to the seawater environment. A total of 47 unique genera were observed to comprise the core taxa community across environment types and sites. No archaeal taxa were observed as part of either the abundant or core taxa. No significant differences were observed for sediment community composition across domains or between sites. For seawater, the bacterial and archaeal community composition was statistically different for the Major Outlet site (p < 0.05), the site closest to a residential area, and the eukaryal community composition was statistically different between all sites (p < 0.05). Our findings highlight the distinct patterns and spatial heterogeneity in microbial communities of a coastal region in Baja California, Mexico.

Molecular Detection and Spatiotemporal Characterization of Labyrinthulomycete Protist Diversity in the Coastal Waters Along the Pearl River Delta

The heterotrophic labyrinthulomycete protists have long been known to play an important role in the nutrient cycling of coastal seawater. Yet, their spatiotemporal abundance and diversity in polluted coastal waters remain poorly discussed, due in part to the paucity of a rapid detection method. To this end, we developed a qPCR detection method based on a newly designed primer pair targeting their 18S rRNA gene. Using this method, we studied the population dynamics of labyrinthulomycete protists in nutrient-rich (Shenzhen Bay) and low-nutrient (Daya) coastal habitats along the Pearl River Delta. We found a significantly (P < 0.05) higher abundance of Labyrinthulomycetes in the Shenzhen bay (average 3455 gene copies mL^-1) than that in Daya Bay (average 378 gene copies mL^-1). Their abundance gradient positively correlated (P < 0.05) with the levels of inorganic nitrogen and phosphates. Further characterization of the molecular diversity of these protists in Shenzhen Bay using different primer sets revealed the presence of several genera besides a large number of unclassified OTUs. Regardless of the primer biases, our results show significant (P < 0.05) spatiotemporal changes in the molecular abundance and diversity of these heterotrophic protists. Overall, this study provides a rapid molecular detection tool for Labyrinthulomycetes and expands our current understanding of their dynamics controlled by physicochemical gradients in coastal waters.

Flow Cytometry for Rapid Enumeration and Biomass Quantification of Thraustochytrids in Coastal Seawaters

Marine fungus-like eukaryotic unicellular protists (thraustochytrids) are considered to play an important role in the marine microbial food web. However, their abundance, distribution, and relative biomass in coastal waters have not yet been examined in detail. By using a flow cytometry method (FCM) for the rapid enumeration of thraustochytrids in nearshore and offshore stations along the Gulf of Bohai, China, we herein expanded current knowledge on their ecological significance. The FCM method allows for the rapid detection and quantification of prokaryotic and eukaryotic cells, but is rarely applied to the enumeration of small eukaryotic protists. Epifluorescence microscopy (EpiM) has been commonly used for the direct detection and enumeration of thraustochytrids; however, this method is time-consuming and inapplicable to a large-scale analysis of complex seawater samples. There is no available FCM method to track the abundance and biomass of thraustochytrids in marine habitats. The FCM enumeration of thraustochytrids in seawater samples ranged between 400 and 4,080 cells mL-1 with a biomass range of 8.15-83.96 μg C L-1. The thraustochytrid biomass contributed 10.9% to 98.1% of the total biomass of the heterotrophic microbial community comprising bacterioplankton and thraustochytrids. Their overall abundance in nearshore stations was significantly different from that in offshore stations (P<0.5). The present results provide an optimized method for the rapid detection and enumeration of thraustochytrids in seawater and facilitate large-scale studies of the ecological role of thraustochytrids in the microbial food web of coastal waters.