Contrasting Mechanisms Determine the Microeukaryotic and Syndiniales Community Assembly in a Eutrophic bay.

Syndiniales is a diverse parasitic group, increasingly gaining attention owing to its high taxonomic diversity in marine ecosystems and inhibitory effects on the dinoflagellate blooms. However, their seasonal dynamics, host interactions, and mechanisms of community assembly are largely unknown, particularly in eutrophic waters. Here, using 18S rRNA gene amplicon sequencing, we intended to elucidate the interactions between Syndiniales and microeukaryotes, as well as community assembly processes in a eutrophic bay. The results showed that Syndiniales group II was dominating throughout the year, with substantially higher abundance in the winter and spring, whereas Syndiniales group I was more abundant in the summer and autumn. Temperature and Dinoflagellata were the most important abiotic and biotic factors driving variations of the Syndiniales community, respectively. The assembly processes of microeukaryotes and Syndiniales were completely different, with the former being controlled by a balance between homogeneous selection and drift and the latter being solely governed by drift. Network analysis revealed that Syndiniales group II had the largest number of interactions with microeukaryotes, and they primarily associated with Dinoflagellata in the winter, while interactions with Chlorophyta and Bacillariophyta increased dramatically in summer and autumn. These findings provide significant insights in understanding the interactions and assembly processes of Syndiniales throughout the year, which is critical in revealing the roles of single-celled parasites in driving protist dynamics in eutrophic waters.

Ecological Dynamics and Co-occurrences Among Prokaryotes and Microeukaryotes in a Diatom Bloom Process in Xiangshan Bay, China.

Diatom blooms can significantly affect the succession of microbial communities, yet little is known about the assembly processes and interactions of microbial communities during autumn bloom events. In this study, we investigated the ecological effects of an autumn diatom bloom on prokaryotic communities (PCCs) and microeukaryotic communities (MECs), focusing on their assembly processes and interactions. The PCCs were largely dominated by Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria, and Flavobacteria, while the MECs primarily included Diatomea, Dinoflagellata, and Chlorophyta. The succession of both PCCs and MECs was mainly driven by this diatom bloom and environmental factors, such as nitrate and silicate. Null modeling revealed that homogeneous selection had a more pronounced impact on the structure of PCCs compared with that of MECs. In particular, drift and dispersal limitation cannot be neglected in the assembly processes of MECs. Co-occurrence network analyses showed that Litorimicrobium, Cercozoa, Marine Group I (MGI), Cryptomonadales, Myrionecta, and Micromonas may affect the bloom process. In summary, these results elucidated the complex, robust interactions and obviously distinct assembly mechanisms of PCCs and MECs during a diatom bloom and extend our current comprehension of the ecological mechanisms and microbial interactions involved in an autumn diatom bloom process.

Interaction and assembly processes of abundant and rare microbial communities during a diatom bloom process.

Diatom blooms can significantly influence the dynamics of microbial communities, yet little is known about the interaction and assembly mechanisms of abundant and rare taxa during bloom process. Here, using 16S rRNA gene amplicon sequencing, we investigated the co-occurrence patterns and assembly processes of abundant and rare microbial communities during an early spring diatom bloom in Xiangshan bay. Our results showed that α-diversity indices in the rare subcommunity (RS) were significantly higher than those in the abundant and common subcommunities. ß-Diversity of the RS was the highest among three subcommunities, and the variation of ß-diversity in the three subcommunities was mainly induced by species turnover, which was also the highest in the RS. The assembly of microbial communities was mainly driven by the neutral processes, but the roles of neutral processes might differ in each subcommunity. Co-occurrence network analysis revealed that abundant and common operational taxonomic units were more often located in central positions within the network. Most of the modules in the network were specific to a particular bloom stage, owing to the succession of Skeletonema costatum. Overall, these findings expand current understanding of the microbial interaction and assembly mechanisms in marine environment suffering harmful algal bloom disturbance.

Divergent Co-occurrence Patterns and Assembly Processes Structure the Abundant and Rare Bacterial Communities in a Salt Marsh Ecosystem.

Understanding how species interaction and assembly processes structure the abundant and rare bacterial biospheres in soils is crucial for predicting how biodiversity influences ecosystem functioning. Here, we profiled the bacterial communities across a salt marsh ecosystem gradient to investigate the co-occurrence patterns across taxa and the relative influence of ecological processes mediating the assembly of the abundant and rare biospheres in soil. Our results revealed abundant taxa to be ubiquitous across all sites, whereas the distributions of the rare taxa were relatively more site specific. The α-diversity indices and ß-diversity of rare subcommunities were significantly higher than those of the abundant subcommunities. Besides, both the taxonomic and functional composition of soil bacterial communities differed significantly between the two biospheres. Furthermore, the influence of stochasticity differed in each subcommunity. In particular, stochastic processes were relatively more important in constraining the assembly of rare taxa. Co-occurrence network analysis revealed that a few abundant taxa occupy central nodes within the networks, possibly indicating crucial roles as keystone taxa. Collectively, these findings suggest that abundant and rare bacterial biospheres have distinct distributions underpinned by a dynamic interplay of ecological processes and taxon co-occurrence patterns.IMPORTANCE Estuarine salt marshes are highly productive ecosystems subjected to regular disturbances by hydrodynamic exchange. However, little is known about how distinct assembly processes and co-occurrence of taxa influence the structure of the abundant and rare bacterial biospheres in these soil systems. This study aims at unravelling these intricacies by studying a typical estuarine salt marsh located in Hangzhou Bay, China. Our study provides important pieces of evidence on the diverse distribution of rare and abundant bacterial biospheres. We show that a few abundant taxa are central nodes in species co-occurrence, potentially playing important roles as keystone species in the system. In addition, we highlight a dynamic interplay of assembly processes structuring these two subcommunities.

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

Marine planktonic bacteria and archaea commonly exhibit pronounced seasonal succession in community composition. But the existence of seasonality in their assembly processes and between-domain differences in underlying mechanism are largely unassessed. Using a high-coverage sampling strategy (including single sample for each station during four cruises in different seasons), 16S rRNA gene sequencing, and null models, we investigated seasonal patterns in the processes governing spatial turnover of bacteria and archaea in surface coastal waters across a sampling grid over ~300 km in the East China Sea. We found that archaea only bloomed in prokaryotic communities during autumn and winter cruises. Seasonality mostly overwhelmed spatial variability in the compositions of both domains. Bacterial and archaeal communities were dominantly governed by deterministic and stochastic assembly processes, respectively, in autumn cruise, probably due to the differences in niche breadths (bacteria < archaea) and relative abundance (bacteria > archaea). Stochasticity dominated assembly mechanisms of both domains but was driven by distinct processes in winter cruise. Determinism-dominated assembly mechanisms of bacteria rebounded in spring and summer cruises, reflecting seasonal variability in bacterial community assembly. This could be attributed to seasonal changes in bacterial niche breadths and habitat heterogeneity across the study area. There were seasonal changes in environmental factors mediating the determinism-stochasticity balance of bacterial community assembly, holding a probability of the existence of unmeasured mediators. Our results suggest contrasting assembly mechanisms of bacteria and archaea in terms of determinism-vs.-stochasticity pattern and its seasonality, highlighting the importance of seasonal perspective on microbial community assembly in marine ecosystems.

Bacterial Community Assembly in a Typical Estuarine Marsh with Multiple Environmental Gradients.

Bacterial communities play essential roles in estuarine marsh ecosystems, but the interplay of ecological processes underlying their community assembly is poorly understood. Here, we studied the sediment bacterial communities along a linear gradient extending from the water-land junction toward a high marsh, using 16S rRNA gene amplicon sequencing. Bacterial community compositions differed significantly between sediment transects. Physicochemical properties, particularly sediment nutrient levels (i.e., total nitrogen [TN] and available phosphorus [AP]), as well as sediment physical structure and pH (P < 0.05), were strongly associated with the overall community variations. In addition, the topological properties of bacterial cooccurrence networks varied with distance to the water-land junction. Both node- and network-level topological features revealed that the bacterial network of sediments farthest from the junction was less intense in complexity and interactions than other sediments. Phylogenetic null modeling analysis showed a progressive transition from stochastic to deterministic community assembly for the water-land junction sites toward the emerging terrestrial system. Taken together, data from this study provide a detailed outline of the distribution pattern of the sediment bacterial community across an estuarine marsh and inform the mechanisms and processes mediating bacterial community assembly in marsh soils.IMPORTANCE Salt marshes represent highly dynamic ecosystems where the atmosphere, continents, and the ocean interact. The bacterial distribution in this ecosystem is of great ecological concern, as it provides essential functions acting on ecosystem services. However, ecological processes mediating bacterial assembly are poorly understood for salt marshes, especially the ones located in estuaries. In this study, the distribution and assembly of bacterial communities in an estuarine marsh located in south Hangzhou Bay were investigated. The results revealed an intricate interplay between stochastic and deterministic processes mediating the assembly of bacterial communities in the studied gradient system. Collectively, our findings illustrate the main drivers of community assembly, taking into consideration changes in sediment abiotic variables and potential biotic interactions. Thus, we offer new insights into estuarine bacterial communities and illustrate the interplay of ecological processes shaping the assembly of bacterial communities in estuarine marsh ecosystems.

Archaeal biogeography and interactions with microbial community across complex subtropical coastal waters.

Marine Archaea are crucial in biogeochemical cycles, but their horizontal spatial variability, assembly processes, and microbial associations across complex coastal waters still lack characterizations at high coverage. Using a dense sampling strategy, we investigated horizontal variability in total archaeal, Thaumarchaeota Marine Group (MG) I, and Euryarchaeota MGII communities and associations of MGI/MGII with other microbes in surface waters with contrasting environmental characteristics across ~200 km by 16S rRNA gene amplicon sequencing. Total archaeal communities were extremely dominated by MGI and/or MGII (98.9% in average relative abundance). Niche partitioning between MGI and MGII or within each group was found across multiple environmental gradients. "Selection" was more important than "dispersal limitation" in governing biogeographic patterns of total archaeal, MGI, and MGII communities, and basic abiotic parameters (such as salinity) and inorganic/organic resources as a whole could be the main driver of "selection". While "homogenizing dispersal" also considerably governed their biogeography. MGI-Nitrospira assemblages were speculatively responsible for complete nitrification. MGI taxa commonly had negative correlations with members of Synechococcus but positive correlations with members of eukaryotic phytoplankton, suggesting that competition or synergy between MGI and phytoplankton depends on specific MGI-phytoplankton assemblages. MGII taxa showed common associations with presumed (photo)heterotrophs including members of SAR11, SAR86, SAR406, and Candidatus Actinomarina. This study sheds light on ecological processes and drivers shaping archaeal biogeography and many strong MGI/MGII-bacterial associations across complex subtropical coastal waters. Future efforts should be made on seasonality of archaeal biogeography and biological, environmental, or ecological mechanisms underlying these statistical microbial associations.

Microbial Community Dynamics and Assembly Follow Trajectories of an Early-Spring Diatom Bloom in a Semienclosed Bay.

Harmful algal blooms (HABs) are serious ecological disasters in coastal areas, significantly influencing biogeochemical cycles driven by bacteria. The shifts in microbial communities during HABs have been widely investigated, but the assembly mechanisms of microbial communities during HABs are poorly understood. Here, using 16S rRNA gene amplicon sequencing, we analyzed the microbial communities during an early-spring diatom bloom, in order to investigate the dynamics of microbial assembly processes. Rhodobacteraceae, Flavobacteriaceae, and Microbacteriaceae were the main bacterial families during the bloom. The 30 most abundant operational taxonomic units (OTUs) segregated into 4 clusters according to specific bloom stages, exhibiting clear successional patterns during the bloom process. The succession of microbial communities correlated with changes in the dynamics of algal species. Based on the ß-nearest taxon distance, we constructed a simulation model, which demonstrated that the assembly of microbial communities shifted from strong heterogenous selection in the early stage of the bloom to stochasticity in the middle stage and then to strong homogeneous selection in the late and after-bloom stages. These successions were driven mainly by chlorophyll a contents, which were affected mainly by Skeletonema costatum Moreover, functional prediction of microbial communities showed that microbial metabolic functions were significantly related to nitrogen metabolism. In summary, our results clearly suggested a dominant role of determinacy in microbial community assembly in HABs and will facilitate deeper understanding of the ecological processes shaping microbial communities during the algal bloom process.IMPORTANCE Harmful algal blooms (HABs) significantly influence biogeochemical cycles driven by bacteria. The shifts in microbial communities during HABs have been studied intensively, but the assembly mechanisms of microbial communities during HABs are poorly understood, with limited investigation of the balance of deterministic and stochastic processes in shaping microbial communities in HABs. In this study, the dynamics and assembly of microbial communities in an early-spring diatom bloom process were investigated. Our data both confirm previously observed general microbial successional patterns and show new detailed mechanisms for microbial assembly in HABs. These results will facilitate deeper understanding of the ecological processes shaping microbial communities in HABs. In addition, predictions of metabolic potential in this study will facilitate understanding of the influence of HABs on nitrogen metabolism in marine environments.

Gracilimonas amylolytica sp. nov., isolated from deep-sea sediment.

A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium, designated LA399T, was isolated from deep-sea sediment collected from the Pacific Ocean. Cells of strain LA399T grew in the medium containing 0-10.0 % of NaCl (w/v; optimum 3.0-5.0 %), pH 6.5-8.0 (optimum 7.0) and 20-40 °C (optimum 37 °C). Aesculin, gelatin, starch and Tween 80 were hydrolysed. Strain LA399T was closely related to Gracilimonas halophila WDS2C40T (97.0 % sequence similarity), Gracilimonas mengyeensis YIM J14T (96.4 %), Gracilimonas rosea CL-KR2T (96.4 %) and Gracilimonas tropica DSM 19535T (96.0 %), and exhibited equal or less than 96.0 % sequence similarity to other type strains of species with validly published names. Phylogenetic analyses revealed that strain LA399T clustered with the clade comprising the Gracilimonas species and formed an independent lineage. Strain LA399T contained menaquinone 7 as the sole isoprenoid quinone and iso-C15 : 0, anteiso-C15 : 0, summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and summed feature 9 (iso-C17 : 1ω9c/10-methyl C16 : 0) as the predominant cellular fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid and three unidentified glycolipids. The DNA G+C content was 45.3 mol%. According to the phylogenetic, chemotaxonomic and phenotypic data, it represents a novel species of the genus Gracilimonas, for which the name Gracilimonas amylolytica is proposed. The type strain is LA399T (=CGMCC 1.16248T=KCTC 52885T).

Agaribacterium haliotis gen. nov., sp. nov., isolated from abalone faeces.

A marine bacterium, named strain feces2T, was isolated from the excreted faeces of an abalone, Haliotis discus hannai. The bacterium was Gram-stain-negative, rod-shaped and had a polar flagellum. It formed a white, small and crater-like colony on an agar plate, and had the capability of degrading agar. Activity of oxidase was positive and that of catalase was negative. Strain feces2T grew at 16 to 40 °C with an optimum of 28-30 °C. The nearly full-length 16S rRNA gene of strain feces2T had the greatest sequence similarity of 92.9 % with Marinibactrumhalimedae Q-192T, followed by of 92.8 % with Teredinibacterturnerae T7902T. Phylogenetic analysis indicated that strain feces2T belonged to the family Cellvibrionaceae, representing an independent clade with an uncultured bacterium clone NEP3-15 (98 % sequence similarity of 16S rRNA gene) derived from the phycosphere of Enteromorphaprolifera. The respiratory quinone was ubiquinone Q-8. The predominant fatty acids consisted of summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), C16 : 0 and summed feature 3 (C16 : 1 ω6c/C16 : 1ω7c). The polar lipids were identified as phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified amino phospholipid and four unknown lipids. The genomic DNA G+C content was 50.5 mol%. On the basis of polyphasic characterizations, strain feces2T represented a novel species and a novel genus in the family Cellvibrionaceae of the order Cellvibrionales within the Gammaproteobacteria, for which the name Agaribacteriumhaliotis gen. nov., sp. nov. is proposed, with the type strain being feces2T (=MCCC 1A11750T=KCTC 52708T). [corrected].

Pseudotenacibaculum haliotis gen. nov., sp. nov., a new member within the Tenacibaculum-Polaribacter clade of the family Flavobacteriaceae, isolated from the intestine of adult abalones, Haliotis diversicolor and H. discushannai.

Two rod-shaped marine bacterial strains named FDZSB0410T and FDZWPB0420, were isolated from the intestine of two adult abalone species, Haliotis diversicolor and Haliotis discushannai, respectively. The strains were non-flagellated, motile by gliding, oxidase-positive but catalase-negative, and agar-degrading. The two strains had identical 16S rRNA gene sequences with the highest sequence similarity less than 96.0 % with species of the genera Tenacibaculumand Polaribacter within the family Flavobacteriaceae. Phylogenetic analysis indicated the strains represented an independent cluster neighbouring with the species of the genera Tenacibaculum and Polaribacter. Strain FDZSB0410T can grow under conditions at 15 to 37 °C with optimum of 30 °C, salinity range from 3 to 4 % (NaCl, w/v) with optimum of 3 %, and pH range from 7 to 8 with optimum of pH 7. The predominant fatty acids of strain FDZSB0410T consisted of iso-C15 : 0, iso-C15 :1 G, summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c), iso-C13 : 0, iso-C17 : 0 3-OH, and iso-C15 : 0 3-OH. The ubiquinone system detected was MK-6. The flexirubin pigment was absent, but the carotenoid was present. The polar lipids were identified as aminolipid, glycolipid, phosphatidylglycerol, an unknown phospholipid and four unknown lipids. The DNA G+C content was 35.3 mol%. On the basis of the genotypic and phenotypic characterizations, strain FDZSB0410T and strain FDZWPB0420 represent a novel species of a new genus in the family Flavobacteriaceae, for which the name Pseudotenacibaculum haliotis gen. nov., sp. nov. is proposed. The type strain of the type species is FDZSB0410T (=KCTC 52127T=MCCC 1A01897T).

Pseudoalteromonas gelatinilytica sp. nov., isolated from surface seawater.

Three Gram-stain-negative, rod-shaped bacteria, designated strains NH153T, F-2-11 and M-1-78, were isolated from surface seawater of the South China Sea and the East China Sea. The three isolates were able to grow at 15-45 °C (optimum 28-37 °C), but no growth occurred at 4 or 50 °C. The pH range for growth was pH 5.5-9.5 (optimum pH 7.5-8.5). The isolates required sea salts for growth and growth occurred in the presence of 0-10 % (w/v) NaCl (optimum 3-5 %); no growth occurred in the presence of 12.0, 15.0 or 20.0 % (w/v) NaCl. They were positive for hydrolysis of gelatin and Tween 80. The sole respiratory quinone was ubiquinone-8 (Q-8). The major cellular fatty acids (>10 %) were C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The major polar lipid components were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified glycolipid, one unidentified phospholipid and one unidentified lipid. The genomic DNA G+C content of strain NH153T was 41.4 mol%. Based on 16S rRNA gene sequence analysis, the isolates were closely related to the type strain of Pseudoalteromonas shioyasakiensis (98.0-98.6 % sequence similarity). The 16S rRNA gene sequence similarities between the three isolates were 98.8-99.7 %. Phylogenetic analysis indicated that they formed a distinct lineage and clustered with P. shioyasakiensis and Pseudoalteromonas arabiensis. The level of DNA-DNA relatedness among the three isolates was 78.0-85.5 %. Strain NH153T exhibited average nucleotide identity values of 93.4 and 84.2 % with respect to P. shioyasakiensisJCM 18891T and P. arabiensisJCM 17292T, respectively. The genome-to-genome distance analysis revealed that strain NH153T shared 52.4 % DNA relatedness with P. shioyasakiensisJCM 18891T and 28.1 % with P. arabiensisJCM 17292T. On the basis of the phenotypic, genotypic and chemotaxonomic characterizations, as well as phylogenetic inference obtained in this study, strains NH153T, F-2-11 and M-1-78 represent a novel species within the genus Pseudoalteromonas, for which the name Pseudoalteromonasgelatinilytica sp. nov. is proposed. The type strain is NH153T (=CGMCC 1.15370T=DSM 100951T), and F-2-11 (=CGMCC 1.15364=DSM 100953) and M-1-78 (=CGMCC 1.15365=DSM 100952), are additional strains of the species.

Bacterial biogeography in the coastal waters of northern Zhejiang, East China Sea is highly controlled by spatially structured environmental gradients.

The underlying mechanisms of microbial community assembly in connective coastal environments are unclear. The coastal water area of northern Zhejiang, East China Sea, is a complex marine ecosystem with multiple environmental gradients, where the distributions and determinants of bacterioplankton communities remain unclear. We collected surface water samples from 95 sites across eight zones in this area for investigating bacterial community with 16S rRNA gene high-throughput sequencing. Bacterial alpha-diversity exhibits strong associations with water chemical parameters and latitude, with 75.5% of variation explained by suspended particle. The composition of dominant phyla can group the sampling sites into four bacterial provinces, and most key discriminant phyla and families/genera of each province strongly associate with specific environmental features, suggesting that local environmental conditions shape the biogeographic provincialism of bacterial taxa. At a broader and finer phylogenetic scale, bacterial beta-diversity is dominantly explained by the shared variation of environmental and spatial factors (63.3%); meanwhile, the environmental determinants of bacterial ß-diversity generally exhibit spatially structured patterns, suggesting that bacterial assembly in surface water is highly controlled by spatially structured environmental gradients in this area. This study provides evidence for the unique biogeographic pattern of bacterioplankton communities at an entire scale of this marine ecosystem.

Response of bacterioplankton communities to cadmium exposure in coastal water microcosms with high temporal variability.

Multiple anthropogenic disturbances to bacterial diversity have been investigated in coastal ecosystems, in which temporal variability in the bacterioplankton community has been considered a ubiquitous process. However, far less is known about the temporal dynamics of a bacterioplankton community responding to pollution disturbances such as toxic metals. We used coastal water microcosms perturbed with 0, 10, 100, and 1,000 µg liter(-1) of cadmium (Cd) for 2 weeks to investigate temporal variability, Cd-induced patterns, and their interaction in the coastal bacterioplankton community and to reveal whether the bacterial community structure would reflect the Cd gradient in a temporally varying system. Our results showed that the bacterioplankton community structure shifted along the Cd gradient consistently after a 4-day incubation, although it exhibited some resistance to Cd at low concentration (10 µg liter(-1)). A process akin to an arms race between temporal variability and Cd exposure was observed, and the temporal variability overwhelmed Cd-induced patterns in the bacterial community. The temporal succession of the bacterial community was correlated with pH, dissolved oxygen, NO3 (-)-N, NO2 (-)-N, PO4 (3-)-P, dissolved organic carbon, and chlorophyll a, and each of these parameters contributed more to community variance than Cd did. However, elevated Cd levels did decrease the temporal turnover rate of community. Furthermore, key taxa, affiliated to the families Flavobacteriaceae, Rhodobacteraceae, Erythrobacteraceae, Piscirickettsiaceae, and Alteromonadaceae, showed a high frequency of being associated with Cd levels during 2 weeks. This study provides direct evidence that specific Cd-induced patterns in bacterioplankton communities exist in highly varying manipulated coastal systems. Future investigations on an ecosystem scale across longer temporal scales are needed to validate the observed pattern.

Changes in intestinal bacterial communities are closely associated with shrimp disease severity.

Increasing evidence has revealed a close association between intestinal bacterial communities and human health. However, given that host phylogeny shapes the composition of intestinal microbiota, it is unclear whether changes in intestinal microbiota structure in relation to shrimp health status. In this study, we collected shrimp and seawater samples from ponds with healthy and diseased shrimps to understand variations in bacterial communities among habitats (water and intestine) and/or health status. The bacterial communities were clustered according to the original habitat and health status. Habitat and health status constrained 14.6 and 7.7 % of the variation in bacterial communities, respectively. Changes in shrimp intestinal bacterial communities occurred in parallel with changes in disease severity, reflecting the transition from a healthy to a diseased state. This pattern was further evidenced by 38 bacterial families that were significantly different in abundance between healthy and diseased shrimps; moderate changes were observed in shrimps with sub-optimal health. In addition, within a given bacterial family, the patterns of enrichment or decrease were consistent with the known functions of those bacteria. Furthermore, the identified 119 indicator taxa exhibited a discriminative pattern similar to the variation in the community as a whole. Overall, this study suggests that changes in intestinal bacterial communities are closely associated with the severity of shrimp disease and that indicator taxa can be used to evaluate shrimp health status.

Biogeography of the sediment bacterial community responds to a nitrogen pollution gradient in the East China Sea.

Patterns of microbial distribution represent the integrated effects of historical and biological processes and are thus a central issue in ecology. However, there is still active debate on whether dispersal limitation contributes to microbial diversification in strongly connected systems. In this study, sediment samples were collected along a transect representing a variety of seawater pollution levels in the East China Sea. We investigated whether changes in sediment bacterial community structures would indicate the effects of the pollution gradient and of dispersal limitation. Our results showed consistent shifts in bacterial communities in response to pollution. More geographically distant sites had more dissimilar communities (r = -0.886, P < 0.001) in this strongly connected sediment ecosystem. A variance analysis based on partitioning by principal coordinates of neighbor matrices (PCNM) showed that spatial distance (dispersal limitation) contributed more to bacterial community variation (8.2%) than any other factor, although the environmental factors explained more variance when combined (11.2%). In addition, potential indicator taxa (primarily affiliated with Deltaproteobacteria and Gammaproteobacteria) were identified; these taxa characterized the pollution gradient. This study provides direct evidence that dispersal limitation exists in a strongly connected marine sediment ecosystem and that candidate indicator taxa can be applied to evaluate coastal pollution levels.

The temporal scaling of bacterioplankton composition: high turnover and predictability during shrimp cultivation.

The spatial distribution of microbial communities has recently been reliably documented in the form of a distance-similarity decay relationship. In contrast, temporal scaling, the pattern defined by the microbial similarity-time relationships (STRs), has received far less attention. As a result, it is unclear whether the spatial and temporal variations of microbial communities share a similar power law. In this study, we applied the 454 pyrosequencing technique to investigate temporal scaling in patterns of bacterioplankton community dynamics during the process of shrimp culture. Our results showed that the similarities decreased significantly (P = 0.002) with time during the period over which the bacterioplankton community was monitored, with a scaling exponent of w = 0.400. However, the diversities did not change dramatically. The community dynamics followed a gradual process of succession relative to the parent communities, with greater similarities between samples from consecutive sampling points. In particular, the variations of the bacterial communities from different ponds shared similar successional trajectories, suggesting that bacterial temporal dynamics are predictable to a certain extent. Changes in bacterial community structure were significantly correlated with the combination of Chl a, TN, PO4 (3-), and the C/N ratio. In this study, we identified predictable patterns in the temporal dynamics of bacterioplankton community structure, demonstrating that the STR of the bacterial community mirrors the spatial distance-similarity decay model.

The application of bacterial indicator phylotypes to predict shrimp health status.

The incidence of shrimp disease is closely associated with the microbial composition in surrounding water, but it remains uncertain whether microbial indicator phylotypes are predictive for shrimp health status (healthy or diseased). To test this idea, we combined the data from our previous works, to investigate the feasibility of indicator phylotypes as independent variables to predict the health status during a shrimp culture procedure. The results showed linearly increased dissimilarities (P<0.001) of the bacterioplankton community over time, while the communities dramatically deviated from this defined trend when disease occurred. This sudden shift in the bacterial community appears to cause severe mass mortality of the shrimps. In particular, we created a model to identify indicators that discriminated ponds with diseased shrimp populations from these with healthy shrimp populations. As a result, 13 indicative families were screened, in which seven are healthy indicator and six are diseased indictor. An improved logistic regression model additionally revealed that the occurrences of these indicator families could be predictive of the shrimp health status with a high degree of accuracy (>79 %). Overall, this study provides solid evidences that indicator phylotypes could be served as independent variables for predicting the incidences of shrimp disease.

Ammonia stimulates growth and nitrite-oxidizing activity of Nitrobacter winogradskyi.

The aim of this study was to obtain a nitrite-oxidizing bacterium with high nitrite oxidation activity for controlling nitrite levels. A nitrite-oxidizing bacterium, ZS-1, was isolated from the water of a coastal Pseudosciaena crocea-rearing pond. The strain was identified as Nitrobacter winogradskyi based on the phylogenetic analyses of the 16S ribosomal ribonucleic acid gene and nxrA sequence of ZS-1. Under aerobic condition, the nitrite-oxidizing activity of ZS-1 did not change considerably in the range of pH 7-9, but was strongly inhibited by lower (pH = 6) and higher (pH = 10) pH values. The optimum temperature range is 25-32 °C. Lower temperature made the adaptive phase of ZS-1 longer but did not affect its maximum nitrite oxidization rate. The nitrite-oxidizing activity of ZS-1 started to be inhibited by ammonia and nitrate when the concentrations of ammonia and nitrate reached 25 mg L-1 and 100 mg L-1, respectively. The inhibition was stronger with higher concentration of ammonia or nitrate. The nitrite-oxidizing activity of ZS-1, however, was not inhibited by high concentration of nitrite (500 mg L-1). The nitrite-oxidizing activity of ZS-1 was increased by low ammonia concentration (1 mg L-1 to 10 mg L-1).