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Sucrose is an effective carbon source for creating more reliable and environmentally friendly conditions for shrimp growth by regulating bacteria in biofloc-based culture systems. However, the influence of sucrose addition on the interaction, co-occurrence networks, and assembly mechanisms of bacterial communities in biofloc-based culture systems remains largely unknown. Here, we comprehensively investigated the effects of sucrose addition on bacterial communities in three habitats (water, bioflocs, and gut). The bacterial community structures and compositions of these three habitats became more similar in groups with sucrose addition, compared with those in controls. More than 50% gut bacterial communities were mainly derived from water and biofloc communities in the sucrose addition groups, but only about 33% bacterial communities migrated from water and biofloc to the gut in the control culture system. Sucrose addition accordantly enriched core taxa belonging to the phylum Actinobacteria and the families Rhodobacteraceae and Flavobacteriaceae in water, biofloc, and gut habitats. These core taxa were important for maintaining bacterial network stability in the sucrose addition culture systems and some were identified as keystone taxa for improving shrimp growth. Furthermore, after sucrose addition, gut bacterial community assembly from water and biofloc was dominated by the heterogeneous select with the ratios of 55–91% and 67–83%, respectively, indicating that sucrose addition can directionally shape the bacterial assembly of the shrimp culture system. These results provide a basis for selectively regulating certain beneficial taxa to improve shrimp growth in culture systems.

Background Microbiome assembly in early life may have a long-term impact on host health. Larval nursery is a crucial period that determines the success in culture of Litopenaeus vannamei, the most productive shrimp species in world aquaculture industry. However, the succession patterns and assembly mechanisms of larval shrimp bacterial community still lack characterization at a fine temporal scale. Here, using a high-frequency sampling strategy and 16S rRNA gene amplicon sequencing, we investigated dynamics of larval shrimp bacterial community and its relationship with bacterioplankton in the rearing water across the whole developmental cycle in a realistic aquaculture practice. Results Alpha-diversity of larval shrimp bacteria showed a U-shaped pattern across the developmental cycle with the stages zoea and mysis as the valley. Correspondingly, the compositions of dominant bacterial taxa at the stages nauplius and early postlarvae were more complex than other stages. Remarkably, Rhodobacteraceae maintained the overwhelming dominance after the mouth opening of larvae (zoea I~early postlarvae). The taxonomic and phylogenetic compositions of larval bacterial community both showed stage-dependent patterns with higher rate of taxonomic turnover, suggesting that taxonomic turnover was mainly driven by temporal switching among closely related taxa (such as Rhodobacteraceae taxa). The assembly of larval bacteria was overall governed by neutral processes (dispersal among individuals and ecological drift) at all the stages, but bacterioplankton also had certain contribution during three sub-stages of zoea, when larval and water bacterial communities were most associated. Furthermore, the positive host selection for Rhodobacteraceae taxa from the rearing water during the zoea stage and its persistent dominance and large predicted contribution to metabolic potentials of organic matters at post-mouth opening stages suggest a crucial role of this family in larval microbiome and thus a potential source of probiotic candidates for shrimp larval nursery. Conclusions Our results reveal pronounced succession patterns and dynamic assembly processes of larval shrimp bacterial communities during the developmental cycle, highlighting the importance of the mouth opening stage from the perspective of microbial ecology. We also suggest the possibility and potential timing in microbial management of the rearing water for achieving the beneficial larval microbiota in the nursery practice.

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 β-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.

Increasing the C/N ratio of input feed has been reported as a practical approach for improving water quality and enhancing shrimp growth through changing the bacterial community of rearing water. However, little is known about the effects of different C/N ratios of feed input on the intestinal microbiota and metabolome of shrimp. In the present study, the effects of three different C/N ratio levels (CN6, CN10, and CN15) maintained by adding sucrose on the growth, intestinal microbiota and metabolome of Litopenaeus vannamei, and bioflocs formation were investigated after 17 days of feeding. The results indicated that higher C/N ratio (10 and 15), especially CN15, of feed input significantly enhance the length and weight of shrimp individuals accompanied by a significant accumulation of bioflocs, compared to that of CN6. The increase of C/N ratio input decreased the α-diversity of the intestinal microbiota and changed the microbial community structure through increasing the relative abundance of Actinobacteria, Rhodobacteraceae (mainly consist of Roseobacter and Paracoccus groups), Alteromonadaceae, and inhibiting the growth of Cyanobacteria, certain Rhodobacteraceae, Mycoplasmataceae and Vibrio. The change of microbial community caused by increasing C/N ratio input was closely associated with various bioactive metabolites of flavonoids, benzenoids, prenol lipids, and indole derivatives, which are benefit for shrimp growth either as an antimicrobial agent or as a nutrient component. Overall, this study demonstrated that manipulating high C/N ratio of feed input helps to the growth of shrimp through increasing the relative abundance of potential beneficial bacteria and the accumulation of various bioactive metabolites to suppress the growth of detrimental bacteria.

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 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

Microbial fermentation can increase the water-soluble protein (WSP) contents of soybean meal, but the microbial community compositions and its functions remain unclear during the fermentation of soybean meal. In this study, the soybean meal was naturally fermented and the dynamics of bacterial community structure were determined. The results showed that natural fermentation can significantly increase the WSP content and digestive enzyme activities of soybean meal. The bacterial diversity indexes of soybean meal were increased and the community structure was significantly changed after fermentation. The bacterial community composition mainly consisted of Pseudomonas before fermentation, but it was almost completely replaced by Bacillus after 24 h of fermentation. The key operational taxonomic unit (OTU) for fermentation was screened as OTU161 from Bacillus, and its candidate strain was isolated from the fermented soybean meal and identified as Bacillus amyloliquefaciens ZB. Bioaugmented inoculation of ZB significantly increased the WSP content by 110.0%, 47.2%, and 473.7%, respectively, after 24, 72, and 96 h of fermentation and digestive enzyme activities by 16.1–41.8% during 24–48 h of fermentation, and shorten the fermentation time, compared to natural fermentation.

Biofloc technology (BFT) has been widely studied and applied in aquaculture, but the bacterial community compositions (BCCs) of bioflocs with different sizes and their associations with the shrimp gut microbiota remain unclear. In this study, bacterial communities of shrimp gut and the bioflocs with three different size-fractions (BS, 100 μm) were investigated by MiSeq sequencing technique. Significantly different bacterial communities were observed between the large (> 20 μm) and small ( 20 μm). A majority of these taxa were strongly correlated with shrimp health or water environmental parameters. However, some candidate pathogens (i.e., Vibrionaceae, Mycoplasmataceae and Pseudoalteromonadaceae) were overrepresented in small-sized bioflocs (

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 β-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.

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 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).

Coexistence of heavy metals and organic contaminants in coastal ecosystems may lead to complicated circumstances in ecotoxicological assessment for biological communities due to potential interactions of contaminants. Consequences of metals and polycyclic aromatic hydrocarbons (PAHs) co-contamination on coastal marine microbes at the community level were paid less attention. We chose cadmium (Cd) and phenanthrene (PHE) as representatives of metals and PAHs, respectively, and mimicked contaminations using coastal water microcosms spiked with Cd (1 mg/L), PHE (1 mg/L), and their mixture over two weeks. 16S rRNA gene amplicon sequencing was used to compare individual and cumulative effects of Cd and PHE on temporal succession of bacterioplankton communities. Although we found dramatic impacts of dimethylsulfoxide (DMSO, used as a carrier solvent for PHE) on bacterial α-diversity and composition, the individual and cumulative effects of Cd and PHE on bacterial α-diversity were temporally variable showing an antagonistic pattern at early stage in the presence of DMSO. Temporal succession of bacterial community composition (BCC) was associated with temporal variability of water physicochemical parameters, each of which explained more variation in BCC than two target contaminants did. However, Cd, PHE, and their mixture distinctly altered the successional trajectories of BCC, while only the effect of Cd was retained at the end of experiment, suggesting certain resilience in BCC after the complete dissipation of PHE along the temporal trajectory. Moreover, bacterial assemblages at the genus level associated with the target contaminants were highly time-dependent and more unpredictable in the co-contamination group, in which some genera possessing hydrocarbon-degrading members might contribute to PHE degradation. These results provide preliminary insights into how co-exposure of Cd and PHE phylogenetically alters successional trajectories of bacterioplankton communities in the manipulated coastal water microcosms.

Understanding the underlying mechanisms that shape the temporal dynamics of a microbial community has important implications for predicting the trajectory of an ecosystem’s response to anthropogenic disturbances. Here, we evaluated the seasonal dynamics of bacterioplankton community composition (BCC) following more than three decades of mariculture disturbance in Xiangshan Bay. Clear seasonal succession and site (fish farm and control site) separation of the BCC were observed, which were primarily shaped by temperature, dissolved oxygen and sampling time. However, the sensitive bacterial families consistently changed in relative abundance in response to mariculture disturbance, regardless of the season. Temporal changes in the BCC followed the time-decay for similarity relationship at both sites. Notably, mariculture disturbance significantly (P

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 β-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.

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.

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 (P0.001) 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.

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.

Five isolates of a previously undescribed species of purple non-sulfur phototrophic bacteria were characterized. They were Gram-negative, had mobile, budding vibrioid cells and contained lamellar intracytoplasmic membranes. Cultures produced red pigments in the light. Live cells of photosynthetic cultures exhibited absorption maxima at 382, 460-464, 494-496, 534-538, 596, 804-806 and 870-874 nm, indicating the presence of bacteriochlorophyll a and carotenoids belonging to the spirilloxanthin series in cells. The new isolates grew anaerobically or microaerobically in the light, but not aerobically in the dark. Optimal growth occurred at 35-40 degrees C and at pH 6.5-8.5. Various organic compounds were used as photosynthetic electron donors and carbon sources. Sulfate was used as sulfur source for growth. Ubiquinone 10 was synthesized as the major quinone. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain gc(T), a representative of the new isolates, was closest to Rhodopseudomonas palustris, with a similarity of 97.5%. DNA-DNA hybridization further distinguished strain gc(T) from Rhodopseudomonas palustris at the species level. Therefore, the name Rhodopseudomonas faecalis sp. nov. was proposed for the new isolates. The type strain is gc(T) ( = AS1.2176(T) = JCM 11668(T)).

Acid- and aluminum (Al)-tolerant microorganisms were isolated from tea fields, from which six strains were selected and identified as Cryptococcus humicola, Rhodotorula glutinis, Aspergillus flavus Link, Penicillium sp., Penicillium janthinellum Biourge and Trichoderma asperellum. They were tolerant to Al up to 100-200 mM and could grow at low pH, 2.5-2.2. In a glucose medium (pH 3.5) the pH of the spent medium decreased to below 3.0. The toxic inorganic monomeric Al in the spent medium decreased with three strains (A. flavus F-6b, Penicillium sp. F-8b and P. janthinellum F-13), but the total Al remained constant for all strains. In a soil extract medium (pH 3.5), the pH of the spent medium of all strains increased to around 6.0-7. 2 and total Al in the spent medium was removed by precipitation due to pH increase. Thus, different tolerance mechanisms were suggested in glucose and soil extract media.

Many reports have shown that the composition of the bacterioplankton community can serve as a biological indicator to evaluate the occurrence of shrimp diseases. However, the distribution, diversity, and function of planktonic actinobacteria in shrimp ponds are still poorly understood. In this study, a prototype of a 16S rRNA gene-based taxonomic microarray was developed and evaluated for monitoring of planktonic actinobacteria in shrimp ponds. The prototype microarray is composed of 30 probes that target ten dominant families of planktonic actinobacteria found in shrimp ponds. The specificity of the actinobacterial microarray was validated by a set of control hybridizations with 16S rRNA genes clones. The prototype microarray was subsequently tested with two seawater samples from ponds with diseased shrimp populations (PDS) and ponds with healthy shrimp populations (PHS). The actinobacteria hybridization profiles revealed a lower abundance of Microbacteriaceae and a higher abundance of Mycobacteriaceae in PDS than in PHS. The changes in planktonic actinobacterial communities were validated by pyrosequencing data. These results support the utility of the microarray for monitoring planktonic actinobacteria in shrimp ponds and aquaculture environments.