Natural assemblages of marine proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter

Microbial community and extracellular polymeric substance dynamics in arid-zone temporary pan ecosystems

Microbial extracellular polymeric substances (EPS) are an important component in sediment ecology. However, most research is highly skewed towards the northern hemisphere and in more permanent systems. This paper investigates EPS (i.e., carbohydrates and proteins) dynamics in arid Austral zone temporary pans sediments. Colorimetric methods and sequence-based metagenomics techniques were employed in a series of small temporary pan ecosystems characterised by alternating wet and dry hydroperiods. Microbial community patterns of distribution were evaluated between seasons (hot-wet and cool-dry) and across depths (and inferred inundation period) based on estimated elevation. Carbohydrates generally occurred in relatively higher proportions than proteins; the carbohydrate:protein ratio was 2.8:1 and 1.6:1 for the dry and wet season respectively, suggesting that EPS found in these systems was largely diatom produced. The wet- hydroperiods (Carbohydrate mean 102 μg g-1; Protein mean 65 μg g-1) supported more EPS production as compared to the dry- hydroperiods (Carbohydrate mean 73 μg g-1; Protein mean 26 μg g-1). A total of 15,042 Unique Amplicon Sequence Variants (ASVs) were allocated to 51 bacterial phyla and 1127 genera. The most abundant genera had commonality in high temperature tolerance, with Firmicutes, Actinobacteria and Proteobacteria in high abundances. Microbial communities were more distinct between seasons compared to within seasons which further suggested that the observed metagenome functions could be seasonally driven. This study's findings implied that there were high levels of denitrification by mostly nitric oxide reductase and nitrite reductase enzymes. EPS production was high in the hot-wet season as compared to relatively lower rates of nitrification in the cool-dry season by ammonia monooxygenases. Both EPS quantities and metagenome functions were highly associated with availability of water, with high rates being mainly associated with wet- hydroperiods compared to dry- hydroperiods. These data suggest that extended dry periods threaten microbially mediated processes in temporary wetlands, with implications to loss of biodiversity by desiccation.

Dynamic patterns of carbohydrate metabolism genes in bacterioplankton during marine algal blooms

Carbohydrates play a pivotal role in nutrient recycling and regulation of algal-bacterial interactions. Despite their ecological significance, the intricate molecular mechanisms governing regulation of phycosphere carbohydrates by bacterial taxa linked with natural algal bloom have yet to be fully elucidated. Here, a comprehensive temporal metagenomic analysis was conducted to explore the carbohydrate-active enzyme (CAZyme) genes in two discrete algal bloom microorganisms (Gymnodinium catenatum and Phaeocystis globosa) across three distinct bloom stages: pre-bloom, peak bloom, and post-bloom. Elevated levels of extracellular carbohydrates, primarily rhamnose, galactose, glucose, and arabinose, were observed during the initial and post-peak stages. The prominent CAZyme families identified-glycoside hydrolases (GH) and carbohydrate-binding modules (CBMs)-were present in both algal bloom occurrences. In the G. catenatum bloom, GH23/24 and CBM13/14 were prevalent during the pre-bloom and peak bloom stages, whereas GH2/3/30 and CBM12/24 exhibited increased prevalence during the post-bloom phase. In contrast, the P. globosa bloom had a dominance of GH13/23 and CBM19 in the initial phase, and this was succeeded by GH3/19/24/30 and CBM54 in the later stages. This gene pool variation-observed distinctly in specific genera-highlighted the dynamic structural shifts in functional resources driven by temporal alterations in available substrates. Additionally, ecological linkage analysis underscored a correlation between carbohydrates (or their related genes) and phycospheric bacteria, hinting at a pattern of bottom-up control. These findings contribute to understanding of the dynamic nature of CAZymes, emphasizing the substantial influence of substrate availability on the metabolic capabilities of algal symbiotic bacteria, especially in terms of carbohydrates.

Toxicity of three microcystin variants on the histology, physiological and metabolism of hepatopancreas and intestinal microbiota of Litopenaeus vannamei

Microcystins (MCs) are prevalent harmful contaminants within shrimp aquaculture systems, exhibiting a diverse array of variants. Gut microbiota can engage in mutual interactions with the host through the gut-liver axis. In this study, the shrimp Litopenaeus vannamei were subjected to three different variants of MCs (LR, YR, RR) at a concentration of 1 μg/L each, and elucidated the alterations in both intestinal microbiota and hepatopancreas physiological homeostasis. The results showed that all three variants of MCs prompted histological alterations in the hepatopancreas, induced elevated levels of oxidative stress biomarkers (H2O2, T-SOD, and CAT), disturbed the transcription levels of immune-related genes (Crus, ALF, and Lys), along with an increase in apoptotic genes (Casp-3 and P53). Furthermore, the metabolic profiles of the hepatopancreas were perturbed, particularly in amino acid metabolism such as "lysine degradation" and "β-alanine metabolism"; the mTOR and FoxO signaling were also influenced, encompassing alterations in the transcription levels of related genes. Additionally, the alterations were observed in the intestinal microbiota's diversity and composition, particularly potential beneficial bacteria (Alloprevotella, Bacteroides, Collinsella, Faecalibacterium, and Prevotellaceae UCG-001), which exhibited a positive correlation with the metabolite berberine. These findings reveal that the three MCs variants can impact the health of the shrimp by interfering with the homeostasis of intestinal microbial and hepatopancreas physiology.

Phylogenic diversity of bacteria associated with potentially toxic cyanobacteria Microcystis aeruginosa: a synthesis on its bloom dynamics

The occurrence of toxic bloom-forming cyanobacteria, Microcystis aeruginosa, has been frequently reported worldwide. These colony forming toxic cyanobacteria harbour a wide range of heterotrophic bacterial communities. The present study has attempted to understand the bloom dynamics of M. aeruginosa along with isolating their colony-associated culturable heterotrophic bacteria from two freshwater ponds in south India with a persisting cyanobacterial bloom. The monthly monitoring of these study areas revealed the conducive role of warm, stagnant waters with high nutrients in forming M. aeruginosa bloom. The peak values of temperature, nitrate, and phosphate at station 1 reached up to 30.5 °C, 4.48 mg/L, 1.64 mg/L, and at station 2, 31 °C, 3.45 mg/L, and 0.62 mg/L, respectively. Twenty-eight bacterial isolates belonging to Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Actinobacteria, and Firmicutes were obtained during the study. Among these 28 isolates, Firmicutes was dominant with the M. aeruginosa bloom from both the study areas.

Using UV/peracetic acid as pretreatment for subsequent bio-treatment of antibiotic-containing wastewater treatment: Mitigating microbial inhibition and antibiotic resistance genes proliferation

UV/peracetic acid (PAA) treatment presents a promising approach for antibiotic removal, but its effects on microbial community and proliferation of antibiotic resistance genes (ARGs) during the subsequent bio-treatment remain unclear. Thus, we evaluated the effects of the UV/PAA on tetracycline (TTC) degradation, followed by introduction of the treated wastewater into the bio-treatment system to monitor changes in ARG expression and biodegradability. Results demonstrated effective TTC elimination by the UV/PAA system, with carbon-centered radicals playing a significant role. Crucially, the UV/PAA system not only eliminated antibacterial activity but also inhibited potential ARG host growth, thereby minimizing the emergence and dissemination of ARGs during subsequent bio-treatment. Additionally, the UV/PAA system efficiently removed multi-antibiotic resistant bacteria and ARGs from the bio-treatment effluent, preventing ARGs from being released into the environment. Hence, we propose a multi-barrier strategy for treating antibiotic-containing wastewater, integrating UV/PAA pre-treatment and post-disinfection with bio-treatment. The inhibition of ARGs transmission by the integrated system was verified through actual soil testing, confirming its effectiveness in preventing ARGs dissemination in the surrounding natural ecosystem. Overall, the UV/PAA treatment system offers a promising solution for tackling ARGs challenges by controlling ARGs proliferation at the source and minimizing their release at the end of the treatment process.

Responses of attached bacterial communities to blooms of the swimming shelled pteropod Creseis acicula in Daya Bay, southern China

The shelled pteropod Creseis acicula is a marine pelagic shellfish widely distributed from temperate to tropical seas around the world. From June to July 2020, a C. acicula bloom first happened in the Daya Bay, southern China, and its density reached the highest value (5600 ind. m-3) ever recorded around the world. However, few studies have investigated the responses of bacterial communities to the C. acicula bloom. In the present study, we examined the community profiles of three communities of bacteria including the free-living and particle-attached bacteria in the blooming and reference waters, and bacteria attached to the whole body and shell of C. acicula using a high-throughput sequencing method. The results indicated that the C. acicula bloom had a greater impact on particle-attached bacteria than free-living bacteria. Among the bloom-sensitive particle-attached bacteria, the predominant bacterial phyla were Pseudomonadota, Bacteroidota and Verrucomicrobiota in the blooming areas, whereas they were Actinomycetota and Planctomycetota in the reference areas. Specifically, fecal bacteria Haloferula and Halioglobus spp. were significantly enriched in the blooming waters and accumulated on C. acicula shells. Conversely, the significantly lower relative abundance of Nocardioides sp. in the blooming area and accumulated on the whole body of C. acicula indicated their attachment to particles consumed by C. acicula. Overall, our results suggested that the C. acicula bloom influenced marine bacteria, particularly particle-attached bacteria, by increasing (e.g. providing shells and feces) or decreasing (e.g. filter-feeding the suspended particles) the abundance of available substances.

Microbial communities drive flux of acid orange 7 and crystal violet dyes in water-sediment system

Unchecked dye effluent discharge poses escalating environmental and economic concerns, especially in developing nations. While dyes are well-recognized water pollutants, the mechanisms of their environmental spread are least understood. Therefore, the present study examines the partitioning of Acid Orange 7 (AO7) and Crystal Violet (CV) dyes using water-sediment microcosms and reports that native microbes significantly affect AO7 decolorization and transfer. Both dyes transition from infused to pristine matrices, reaching equilibrium in a fortnight. While microbes influence CV partitioning, their role in decolorization is minimal, emphasizing their varied impact on the environmental fate of dyes. Metagenomic analyses reveal contrasting microbial composition between control and AO7-infused samples. Control water samples displayed a dominance of Proteobacteria (62%), Firmicutes (24%), and Bacteroidetes (9%). However, AO7 exposure led to Proteobacteria reducing to 57% and Bacteroidetes to 3%, with Firmicutes increasing to 34%. Sediment samples, primarily comprising Firmicutes (47%) and Proteobacteria (39%), shifted post-AO7 exposure: Proteobacteria increased to 53%, and Firmicutes dropped to 38%. At the genus level, water samples dominated by Niveispirillum (34%) declined after AO7 exposure, while Bacillus and Pseudomonas increased. Notably, Serratia and Sphingomonas, known for azo dye degradation, rose post-exposure, hinting at their role in AO7 decolorization. Conversely, sediment samples showed a decrease in the growth of Bacillus and an increase in that of Pseudomonas and Serratia. These findings emphasize the significant role of microbial communities in determining the environmental fate of dyes, providing insights on its environmental implications and management.

Light-dark fluctuated metabolic features of diazotrophic and non-diazotrophic cyanobacteria and their coexisting bacteria

Cyanobacteria, the most abundant photosynthetic organisms in oceans, are tightly associated with diverse microbiota. However, the relationships between heterotrophic bacteria and cyanobacteria, particularly the diazotrophic group, are not fully understood. Here, we compared diel gene expressions of N2 fixing cyanobacteria Crocosphaera watsonii WH0003 and non-diazotrophic Synechococcus sp. RS9902 and their associated bacteria using metatranscriptomics approach. WH0003 showed significant up-regulation of O2 restriction and oxidative phosphorylation related genes at nighttime due to large carbon and energy investments for active N2 fixation. In contrast, RS9902 had higher expression for those genes at daytime. The two cyanobacteria hosted distinct bacterial communities with clear separate substrate utilization niches to reduce competition. Light-dark partitioning of nutrient acquisition among the dominant bacterial groups likely contributed to the dynamic balance for community coexistence. Moreover, particle-attached (PA) bacteria in RS9902 largely expressed glycoside hydrolases to hydrolyze complex carbohydrate compounds, while free-living (FL) bacteria priorly assimilated soluble, diffusible molecules. Spatial partitioning of nutrient acquisition between PA and FL bacteria implied that location initially influenced metabolic features of host associated bacteria. Our results advance knowledge on light-dark regulated metabolic activities of diazotrophic and non-diazotrophic cyanobacteria, and provide new insights into the coexisting strategies of different bacterial groups.

Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus

BACKGROUND

Spotting disease infects a variety of sea urchin species across many different marine locations. The disease is characterized by discrete lesions on the body surface composed of discolored necrotic tissue that cause the loss of all surface appendages within the lesioned area. A similar, but separate disease of sea urchins called bald sea urchin disease (BSUD) has overlapping symptoms with spotting disease, resulting in confusions in distinguishing the two diseases. Previous studies have focus on identifying the underlying causative agent of spotting disease, which has resulted in the identification of a wide array of pathogenic bacteria that vary based on location and sea urchin species. Our aim was to investigate the spotting disease infection by characterizing the microbiomes of the animal surface and various tissues.

RESULTS

We collected samples of the global body surface, the lesion surface, lesioned and non-lesioned body wall, and coelomic fluid, in addition to samples from healthy sea urchins. 16S rRNA gene was amplified and sequenced from the genomic DNA. Results show that the lesions are composed mainly of Cyclobacteriaceae, Cryomorphaceae, and a few other taxa, and that the microbial composition of lesions is the same for all infected sea urchins. Spotting disease also alters the microbial composition of the non-lesioned body wall and coelomic fluid of infected sea urchins. In our closed aquarium systems, sea urchins contracted spotting disease and BSUD separately and therefore direct comparisons could be made between the microbiomes from diseased and healthy sea urchins.

CONCLUSION

Results show that spotting disease and BSUD are separate diseases with distinct symptoms and distinct microbial compositions.

Transparent antibiofouling coating to improve the efficiency of Nannochloropsis gaditana and Chlorella sorokiniana culture photobioreactors at the pilot-plant scale

The implementation of industrial-scale facilities for microalgae cultivation is limited due to the high operation costs. One of the main problems in obtaining an efficient and long-lasting microalgae culture system is biofouling. The particular issue when developing antibiofouling surfaces for microalgae cultures is that the material must be transparent. The main purpose of this work was to evaluate the antibiofouling efficiency of a non-toxic polydimethylsiloxane-based coating prepared with polyethylene glycol-based copolymer on different photobioreactors at the pilot-plant scale. The antifouling properties result from the development of a fouling-release coating utilizing hydrogel technology. Nannochloropsis gaditana and Chlorella sorokiniana were cultured outdoors for 3 months over the summer, when biofouling formation is at its highest due to environmental conditions, to test the coating's antibiofouling efficiency. Although biofouling was not completely prevented in either photobioreactor, the coating significantly reduced cell adhesion compared to the polydimethylsiloxane control (70% less adhesion). Therefore, this coating was shown to be a good alternative for constructing efficient closed-photobioreactors at the pilot-plant scale, at least for cultures lasting 3 months.

Suboxic DOM is bioavailable to surface prokaryotes in a simulated overturn of an oxygen minimum zone, Devil's Hole, Bermuda

Oxygen minimum zones (OMZs) are expanding due to increased sea surface temperatures, subsequent increased oxygen demand through respiration, reduced oxygen solubility, and thermal stratification driven in part by anthropogenic climate change. Devil's Hole, Bermuda is a model ecosystem to study OMZ microbial biogeochemistry because the formation and subsequent overturn of the suboxic zone occur annually. During thermally driven stratification, suboxic conditions develop, with organic matter and nutrients accumulating at depth. In this study, the bioavailability of the accumulated dissolved organic carbon (DOC) and the microbial community response to reoxygenation of suboxic waters was assessed using a simulated overturn experiment. The surface inoculated prokaryotic community responded to the deep (formerly suboxic) 0.2 μm filtrate with cell densities increasing 2.5-fold over 6 days while removing 5 μmol L-1 of DOC. After 12 days, the surface community began to shift, and DOC quality became less diagenetically altered along with an increase in SAR202, a Chloroflexi that can degrade recalcitrant dissolved organic matter (DOM). Labile DOC production after 12 days coincided with an increase of Nitrosopumilales, a chemoautotrophic ammonia oxidizing archaea (AOA) that converts ammonia to nitrite based on the ammonia monooxygenase (amoA) gene copy number and nutrient data. In comparison, the inoculation of the deep anaerobic prokaryotic community into surface 0.2 μm filtrate demonstrated a die-off of 25.5% of the initial inoculum community followed by a 1.5-fold increase in cell densities over 6 days. Within 2 days, the prokaryotic community shifted from a Chlorobiales dominated assemblage to a surface-like heterotrophic community devoid of Chlorobiales. The DOM quality changed to less diagenetically altered material and coincided with an increase in the ribulose-1,5-bisphosphate carboxylase/oxygenase form I (cbbL) gene number followed by an influx of labile DOM. Upon reoxygenation, the deep DOM that accumulated under suboxic conditions is bioavailable to surface prokaryotes that utilize the accumulated DOC initially before switching to a community that can both produce labile DOM via chemoautotrophy and degrade the more recalcitrant DOM.

Bacteria-Virus Interactions Are More Crucial in Soil Organic Carbon Storage than Iron Protection in Biochar-Amended Paddy Soils

Iron oxides supposedly provide physicochemical protection for soil organic carbon (SOC) under anoxic conditions. Likewise, biochar can modulate the composition of soil microbial communities. However, how Fe oxides and microbial communities influence the fate of SOC with biochar amendment remains unresolved, especially the effect of the bacteria-virus interaction on SOC dynamics. Here, we performed a four-month pot experiment using rice seedlings with a biochar amendment under waterlogged conditions. Then, soil aggregate sizes were examined to explore the factors influencing the SOC patterns and the underlying mechanisms. We found that biochar altered soil enzyme activities, especially in macroaggregates. Fe oxides and necromass exhibited significant negative relationships with SOC. Bacterial communities were notably associated with viral communities. Here, the keystone ecological cluster (module 1) and keystone taxa in the bacteria-virus network showed significant negative correlations with SOC. However, Fe oxides exhibited substantial positive relationships with module 1. In contrast to the prevailing view, the SOC increase was not primarily driven by Fe oxides but strongly influenced by bacteria-virus interactions and keystone taxa. These findings indicate that biochar governs microbial-mediated SOC accumulation in paddy soil and ascertains the role of viruses in regulating the bacterial community, thus predicting SOC stock.

Exploring the phycosphere of Emiliania huxleyi: From bloom dynamics to microbiome assembly experiments

Coccolithophores have global ecological and biogeochemical significance as the most important calcifying marine phytoplankton group. The structure and selection of prokaryotic communities associated with the most abundant coccolithophore and bloom-forming species, Emiliania huxleyi, are still poorly known. In this study, we assessed the diversity of bacterial communities associated with an E. huxleyi bloom in the Celtic Sea (Eastern North Atlantic), exposed axenic E. huxleyi cultures to prokaryotic communities derived from bloom and non-bloom conditions, and followed the dynamics of their microbiome composition over one year. Bloom-associated prokaryotic communities were dominated by SAR11, Marine group II Euryarchaeota and Rhodobacterales and contained substantial proportions of known indicators of phytoplankton bloom demises such as Flavobacteriaceae and Pseudoalteromonadaceae. The taxonomic richness of bacteria derived from natural communities associated with axenic E. huxleyi rapidly shifted and then stabilized over time. The succession of microorganisms recruited from the environment was consistently dependent on the composition of the initial bacterioplankton community. Phycosphere-associated communities derived from the E. huxleyi bloom were highly similar to one another, suggesting deterministic processes, whereas cultures from non-bloom conditions show an effect of stochasticity. Overall, this work sheds new light on the importance of the initial inoculum composition in microbiome recruitment and elucidates the temporal dynamics of its composition and long-term stability.

Changes in Hemolymph Microbiota of Chinese Mitten Crab (Eriocheir sinensis) in Response to Aeromonas hydrophila or Staphylococcus aureus Infection

The Chinese mitten crab (Eriocheir sinensis) has significant economic potential in both the Chinese domestic and global markets. The hemolymph microbiota is known to play a critical role in regulating physiological and biochemical functions in crustaceans. However, the study of the hemolymph microbiota of E. sinensis in response to infections has not been undertaken. In this study, changes in the composition and function of the hemolymph microbiota in E. sinensis infected with either Staphylococcus aureus (Sa) or Aeromonas hydrophila (Ah) were investigated using 16S rRNA sequencing, with a phosphate buffer saline (PBS) injection serving as the control. Results showed that the dominant hemolymph microbiota of E. sinensis were Proteobacteria, Bacteroidota, and Firmicutes. The relative abundance of the phyla Firmicutes, Bdellovibrionota, and Myxococcota was significantly reduced in both Sa and Ah groups compared to the PBS group. At the genus level, compared to the PBS group, a significant increase in the abundance of Flavobacterium and Aeromonas was found in both Ah and Sa groups. The analysis of the functional profile showed that pathways related to 'cell growth and death', 'metabolism of terpenoids and polyketides', 'cancers', 'lipid metabolism', 'neurodegenerative diseases', 'metabolism of other amino acids', 'xenobiotics biodegradation and metabolism', and 'circulatory system and endocrine system' were predominant in the Ah group. Meanwhile, pathways related to 'metabolism or genetic information progressing', such as 'translation', 'metabolic diseases', and 'cellular processes and signaling', were enriched in the Sa group. This study revealed the effects of pathogens (S. aureus or A. hydrophila) on the maintenance of the hemolymph microbiota in E. sinensis. It shed light on the mechanisms employed by the hemolymph microbiota of E. sinensis under pathogen stimulation.

Effects of Prometryn Exposure on Hepatopancreas Oxidative Stress and Intestinal Flora in Eriocheir sinensis (Crustacea: Decapoda)

There is growing evidence that long-term exposure to prometryn (a widely used herbicide) can induce toxicity in bony fish and shrimp. Our previous study demonstrated its 96 h acute toxicity on the crab Eriocheir sinensis. However, studies on whether longer exposure to prometryn with a lower dose induces toxicity in E. sinensis are scarce. Therefore, we conducted a 20 d exposure experiment to investigate its effects on the hepatopancreas and intestine of E. sinensi. Prometryn reduce the activities of antioxidant enzymes, increase the level of lipid peroxidation and cause oxidative stress. Moreover, long-term exposure resulted in immune and detoxification fatigue, while short-term exposure to prometryn could upregulate the expression of genes related to immunity, inflammation and detoxification. Prometryn altered the morphological structure of the hepatopancreas (swollen lumen) and intestine (shorter intestinal villi, thinner muscle layer and thicker peritrophic membrane). In addition, prometryn changed the species composition of the intestinal flora. In particular, Bacteroidota and Proteobacteria showed a dose-dependent decrease accompanied by a dose-dependent increase in Firmicutes at the phylum level. At the genus level, all exposure groups significantly increased the abundance of Zoogloea and a Firmicutes bacterium ZOR0006, but decreased Shewanella abundance. Interestingly, Pearson correlation analysis indicated a potential association between differential flora and hepatopancreatic disorder. Phenotypic abundance analysis indicated that changes in the gut flora decreased the intestinal organ's resistance to stress and increased the potential for opportunistic infection. In summary, our research provides new insights into the prevention and defense strategies in response to external adverse environments and contributes to the sustainable development of E. sinensis culture.

Metagenomic Insights Reveal the Microbial Diversity and Associated Algal-Polysaccharide-Degrading Enzymes on the Surface of Red Algae among Remote Regions

Macroalgae and macroalgae-associated bacteria together constitute the most efficient metabolic cycling system in the ocean. Their interactions, especially the responses of macroalgae-associated bacteria communities to algae in different geographical locations, are mostly unknown. In this study, metagenomics was used to analyze the microbial diversity and associated algal-polysaccharide-degrading enzymes on the surface of red algae among three remote regions. There were significant differences in the macroalgae-associated bacteria community composition and diversity among the different regions. At the phylum level, Proteobacteria, Bacteroidetes, and Actinobacteria had a significantly high relative abundance among the regions. From the perspective of species diversity, samples from China had the highest macroalgae-associated bacteria diversity, followed by those from Antarctica and Indonesia. In addition, in the functional prediction of the bacterial community, genes associated with amino acid metabolism, carbohydrate metabolism, energy metabolism, metabolism of cofactors and vitamins, and membrane transport had a high relative abundance. Canonical correspondence analysis and redundancy analysis of environmental factors showed that, without considering algae species and composition, pH and temperature were the main environmental factors affecting bacterial community structure. Furthermore, there were significant differences in algal-polysaccharide-degrading enzymes among the regions. Samples from China and Antarctica had high abundances of algal-polysaccharide-degrading enzymes, while those from Indonesia had extremely low abundances. The environmental differences between these three regions may impose a strong geographic differentiation regarding the biodiversity of algal microbiomes and their expressed enzyme genes. This work expands our knowledge of algal microbial ecology, and contributes to an in-depth study of their metabolic characteristics, ecological functions, and applications.

Genomic analysis and chitinase characterization of Vibrio harveyi WXL538: insight into its adaptation to the marine environment

Chitin, the most abundant bio-polymer in seawater, may be utilized by various microorganisms as a carbon source. Vibrios have been regarded as one of the main groups of chitin consumers in the marine carbon cycle and chitinase producers. The organisms are widely distributed in the aquatic environment. However, the co-working mechanism between their chitinases, and whether the chitinase's diversity contributes to their adaption to the environment, needs to be further elucidated. Here, we obtained a chitinolytic strain, Vibrio harveyi WXL538 with eight putative chitinase-coding genes. Five of the genes, i.e., Chi4733, Chi540, Chi4668, Chi5174, and Chi4963, were overexpressed and validated, in which Chi4668, Chi4733 and Chi540 were purified and characterized. The result of Chi4668 was described in our previous study. Endo-chitinase Chi4733 degraded colloidal chitin to produce (GlcNAc)2 and minor (GlcNAc)3. The enzymatic activity of Chi4733 was 175.5 U mg-1 and Kcat/Km was 54.9 s-1 M-1. Chi4733 had its maximum activity at 50°C and pH 4-6, activated by Sr2+, Co2+, Ca2+, and Mg2+ and inhibited by Al3+, Zn2+, Cu2+, Ni2+, and SDS. Exo-chitinase Chi540 degraded colloidal chitin to (GlcNAc)2. The enzymatic activity of Chi540 was 134.5 U mg-1 and Kcat/Km was 54.9 s-1 M-1. Chi540 had its maximum activity at 60°C and pH 6-8, was activated by Sr2+, Ca2+, and Mg2+ but inhibited by K+, Ba2+, Zn2+, Cu2+, Ni2+, SDS and urea. Whole genome analysis of V. harveyi WXL538 and characterization of its chitinase can provide a better understanding of its adaptability to the changing marine environment.

Polymeric carbohydrates utilization separates microbiomes into niches: insights into the diversity of microbial carbohydrate-active enzymes in the inner shelf of the Pearl River Estuary, China

Polymeric carbohydrates are abundant and their recycling by microbes is a key process of the ocean carbon cycle. A deeper analysis of carbohydrate-active enzymes (CAZymes) can offer a window into the mechanisms of microbial communities to degrade carbohydrates in the ocean. In this study, metagenomic genes encoding microbial CAZymes and sugar transporter systems were predicted to assess the microbial glycan niches and functional potentials of glycan utilization in the inner shelf of the Pearl River Estuary (PRE). The CAZymes gene compositions were significantly different between in free-living (0.2-3 μm, FL) and particle-associated (>3 μm, PA) bacteria of the water column and between water and surface sediments, reflecting glycan niche separation on size fraction and selective degradation in depth. Proteobacteria and Bacteroidota had the highest abundance and glycan niche width of CAZymes genes, respectively. At the genus level, Alteromonas (Gammaproteobacteria) exhibited the greatest abundance and glycan niche width of CAZymes genes and were marked by a high abundance of periplasmic transporter protein TonB and members of the major facilitator superfamily (MFS). The increasing contribution of genes encoding CAZymes and transporters for Alteromonas in bottom water contrasted to surface water and their metabolism are tightly related with particulate carbohydrates (pectin, alginate, starch, lignin-cellulose, chitin, and peptidoglycan) rather than on the utilization of ambient-water DOC. Candidatus Pelagibacter (Alphaproteobacteria) had a narrow glycan niche and was primarily preferred for nitrogen-containing carbohydrates, while their abundant sugar ABC (ATP binding cassette) transporter supported the scavenging mode for carbohydrate assimilation. Planctomycetota, Verrucomicrobiota, and Bacteroidota had similar potential glycan niches in the consumption of the main component of transparent exopolymer particles (sulfated fucose and rhamnose containing polysaccharide and sulfated-N-glycan), developing considerable niche overlap among these taxa. The most abundant CAZymes and transporter genes as well as the widest glycan niche in the abundant bacterial taxa implied their potential key roles on the organic carbon utilization, and the high degree of glycan niches separation and polysaccharide composition importantly influenced bacterial communities in the coastal waters of PRE. These findings expand the current understanding of the organic carbon biotransformation, underlying the size-fractionated glycan niche separation near the estuarine system.

Habitat distribution of the genus Belliella in continental waters and the description of Belliella alkalica sp. nov., Belliella calami sp. nov. and Belliella filtrata sp. nov

The genus Belliella belongs to the family Cyclobacteriaceae (order Cytophagales, phylum Bacteroidota) and harbours aerobic chemoheterotrophic bacteria. Members of this genus were isolated from various aquatic habitats, and our analysis based on global amplicon sequencing data revealed that their relative abundance can reach up to 5-10 % of the bacterioplankton in soda lakes and pans. Although a remarkable fraction of the most frequent genotypes that we identified from continental aquatic habitats is still uncultured, five new alkaliphilic Belliella strains were characterized in detail in this study, which were isolated from three different soda lakes and pans of the Carpathian Basin (Hungary). Cells of all strains were Gram-stain-negative, obligate aerobic, rod-shaped, non-motile and non-spore-forming. The isolates were oxidase- and catalase-positive, red-coloured, but did not contain flexirubin-type pigments; they formed bright red colonies that were circular, smooth and convex. Their major isoprenoid quinone was MK-7 and the predominant fatty acids were iso-C_15 : 0, iso-C_17 : 0 3-OH and summed feature 3 containing C_16 : 1  ω6c and/or C_16 : 1  ω7c. The polar lipid profiles contained phosphatidylethanolamine, an unidentified aminophospholipid, an unidentified glycolipid, and several unidentified lipids and aminolipids. Based on whole-genome sequences, the DNA G+C content was 37.0, 37.1 and 37.8 mol % for strains R4-6^T, DMA-N-10a^T and U6F3^T, respectively. The distinction of three new species was confirmed by in silico genomic comparison. Orthologous average nucleotide identity (<85.4 %) and digital DNA-DNA hybridization values (<38.9 %) supported phenotypic, chemotaxonomic and 16S rRNA gene sequence data and, therefore, the following three novel species are proposed: Belliella alkalica sp. nov. (represented by strains R4-6^T=DSM 111903^T=JCM 34281^T=UCCCB122^T and S4-10), Belliella calami sp. nov. (DMA-N-10a^T=DSM 107340^T=JCM 34280^T=UCCCB121^T) and Belliella filtrata sp. nov. (U6F3^T=DSM 111904^T=JCM 34282^T=UCCCB123^T and U6F1). Emended descriptions of species Belliella aquatica, Belliella baltica, Belliella buryatensis, Belliella kenyensis and Belliella pelovolcani are also presented.

Effects of potassium monopersulfate on nitrification activity and bacterial community structure of sponge biocarrier biofilm in Litopenaeus vannamei aquaculture system

Effects of potassium monopersulfate (KMPS) on the nitrification activity, aquacultural water quality and bacterial community structure of sponge biocarriers with pre-cultured biofilm (SBBF) were analysed through shaking flask experiments and L. vannamei aquaculture experiments. Changes in the ammonia oxidation rate (AOR) and nitrite oxidation rate (NOR) of SBBF under six KMPS concentration treatments (0 mg/L, 1 mg/L, 2 mg/L, 3 mg/L, 4 mg/L and 5 mg/L) were studied. The results showed that the AOR and NOR of SBBF treated with high concentrations of KMPS (3 mg/L, 4 mg/L and 5 mg/L) were significantly lower than those of the control group (CK) (p < 0.05). However, compared with the first dosing of NH₄Cl and NaNO₂, the inhibition of AOR and NOR by KMPS on AOR and NOR was weakened after the second and third dosing times. That is, AOR and NOR can recover partially or completely over time. The L. vannamei aquaculture experiment was performed using four concentrations of KMPS (0 mg/L, 2 mg/L, 4 mg/L and 8 mg/L). The results showed that with increasing KMPS dosage, the average and peak concentrations of NH₄⁺-N and NO₂^--N in each treatment significantly increased (P <0.05), and the final body weight of shrimp significantly decreased (P <0.05). Furthermore the highest dose (8.0 mg/L) of KMPS reduced the survival rate by 9.33% compared to the CK. High-throughput sequencing analysis of the biofilm structure showed that the relative abundances of Nitrospirota, Nitrosomonas and Nitrococcus, which are related to nitrogen cycling, and beneficial bacteria including Firmicutes and Bacilli decreased with the addition of KMPS (p<0.05).

Water Mass Controlled Vertical Stratification of Bacterial and Archaeal Communities in the Western Arctic Ocean During Summer Sea-Ice Melting

The environmental variations and their interactions with the biosphere are vital in the Arctic Ocean during the summer sea-ice melting period in the current scenario of climate change. Hence, we analysed the vertical distribution of bacterial and archaeal communities in the western Arctic Ocean from sea surface melt-ponds to deep water up to a 3040 m depth. The distribution of microbial communities showed a clear stratification with significant differences among different water depths, and the water masses in the Arctic Ocean - surface mixed layer, Atlantic water mass and deep Arctic water - appeared as a major factor explaining their distribution in the water column. A total of 34 bacterial phyla were detected in the seawater and 10 bacterial phyla in melt-ponds. Proteobacteria was the dominant phyla in the seawater irrespective of depth, whereas Bacteroidota was the dominant phyla in the melt-ponds. A fast expectation-maximization microbial source tracking analysis revealed that only limited dispersion of the bacterial community was possible across the stratified water column. The surface water mass contributed 21% of the microbial community to the deep chlorophyll maximum (DCM), while the DCM waters contributed only 3% of the microbial communities to the deeper water masses. Atlantic water mass contributed 37% to the microbial community of the deep Arctic water. Oligotrophic heterotrophic bacteria were dominant in the melt-ponds and surface waters, whereas chemoautotrophic and mixotrophic bacterial and archaeal communities were abundant in deeper waters. Chlorophyll and ammonium were the major environmental factors that determined the surface microbial communities, whereas inorganic nutrient concentrations controlled the deep-water communities.

The potential to produce tropodithietic acid by Phaeobacter inhibens affects the assembly of microbial biofilm communities in natural seawater

Microbial secondary metabolites play important roles in biotic interactions in microbial communities and yet, we do not understand how these compounds impact the assembly and development of microbial communities. To address the implications of microbial secondary metabolite production on biotic interactions in the assembly of natural seawater microbiomes, we constructed a model system where the assembly of a natural seawater biofilm community was influenced by the addition of the marine biofilm forming Phaeobacter inhibens that can produce the antibiotic secondary metabolite tropodithietic acid (TDA), or a mutant incapable of TDA production. Because of the broad antibiotic activity of TDA, we hypothesized that the potential of P. inhibens to produce TDA would strongly affect both biofilm and planktonic community assembly patterns. We show that 1.9 % of the microbial composition variance across both environments could be attributed to the presence of WT P. inhibens, and especially genera of the Bacteriodetes were increased by the presence of the TDA producer. Moreover, network analysis with inferred putative microbial interactions revealed that P. inhibens mainly displayed strong positive associations with genera of the Flavobacteriaceae and Alteromonadaceae, and that P. inhibens acts as a keystone OTU in the biofilm exclusively due to its potential to produce TDA. Our results demonstrate the potential impact of microbial secondary metabolites on microbial interactions and assembly dynamics of complex microbial communities.

Active and dormant microorganisms on glacier surfaces

Glacier and ice sheet surfaces host diverse communities of microorganisms whose activity (or inactivity) influences biogeochemical cycles and ice melting. Supraglacial microbes endure various environmental extremes including resource scarcity, frequent temperature fluctuations above and below the freezing point of water, and high UV irradiance during summer followed by months of total darkness during winter. One strategy that enables microbial life to persist through environmental extremes is dormancy, which despite being prevalent among microbial communities in natural settings, has not been directly measured and quantified in glacier surface ecosystems. Here, we use a combination of metabarcoding and metatranscriptomic analyses, as well as cell-specific activity (BONCAT) incubations to assess the diversity and activity of microbial communities from glacial surfaces in Iceland and Greenland. We also present a new ecological model for glacier microorganisms and simulate physiological state-changes in the glacial microbial community under idealized (i) freezing, (ii) thawing, and (iii) freeze-thaw conditions. We show that a high proportion (>50%) of bacterial cells are translationally active in-situ on snow and ice surfaces, with Actinomycetota, Pseudomonadota, and Planctomycetota dominating the total and active community compositions, and that glacier microorganisms, even when frozen, could resume translational activity within 24 h after thawing. Our data suggest that glacial microorganisms respond rapidly to dynamic and changing conditions typical of their natural environment. We deduce that the biology and biogeochemistry of glacier surfaces are shaped by processes occurring over short (i.e., daily) timescales, and thus are susceptible to change following the expected alterations to the melt-regime of glaciers driven by climate change. A better understanding of the activity of microorganisms on glacier surfaces is critical in addressing the growing concern of climate change in Polar regions, as well as for their use as analogues to life in potentially habitable icy worlds.

Natural Variations in the Benthic Environment and Bacterial Communities of Coastal Sediments around Aquaculture Farms in South Korea

The aim of this study was to examine the possible seasonal variations in the nutrients (dissolved inorganic nitrogen-DIN and phosphorus) and benthic bacterial communities in marine aquaculture surrounding sediments. The study areas were Geoje, Tongyeong, and Changwon bays in Korea, which are famous for oysters (Magallana gigas), Halocynthia roretzi, and warty sea squirt (Styela clava) farming, respectively. The study sites included semi-enclosed coastal areas with a low seawater exchange rate. Subtidal sediment samples were collected seasonally from the area surrounding the aquacultures between April and December 2020. Seasonal variations in nutrients were observed, with the highest concentration of DIN in August. For phosphorus, site-specific variations were also observed. To investigate the variations in benthic bacterial communities, the advanced technique of 16S rRNA gene amplicon sequencing was applied, and the results indicated a seasonal variation pattern and predominance of Proteobacteria (59.39-69.73%), followed by Bacteroidetes (6.55-12.85%) and Chloroflexi (2.04-4.50%). This study provides a reference for future studies on natural variations in the benthic environment and bacterial communities in the areas surrounding aquacultures.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-023-01067-8.

Effects of Cryptocaryon irritans infection on the histopathology, oxidative stress, immune response, and intestinal microbiota in the orange-spotted grouper Epinephelus coioides

Cryptocaryon irritans is a parasitic ciliate of marine fish, causing serious mortality and economic loss of grouper. In this study, the orange-spotted grouper (Epinephelus coioides) were separately exposed to C. irritans infection for 72 h at a dose of 5000 or 10000 active theronts per fish, and we evaluated the changes in histopathology, oxidative stress, immune response, and intestinal microbiota composition. The results showed that C. irritans infection caused pathological alteration on the skin, gills, and liver of E. coioides. Oxidative stress responses occurred in the liver and gills, reflected in the corresponding antioxidant enzyme and gene indexes. The mRNA expression levels of inflammation-related genes (IL-1β, IL-6, and IL-8) and the mediators of apoptosis (casp3, casp9, and cytc) were increased in the liver and gills of the fish. C. irritans infection also affected the diversity and composition of intestinal microbiota. Specifically, the relative abundance of Firmicutes was increased, whereas that of Proteobacteria was decreased. Several potentially beneficial bacteria (Pandoraea, Clostridium sensu stricto 1, Christensenellaceae R-7 group, and Weissella) were decreased, whereas pathogenic bacteria (Streptococcus and Acinetobacter) were increased. In conclusion, this study reveals that C. irritans infection caused histopathology, immune disorders, and intestinal microbial community variation in E. coioides.

Toxicological response of Pacific white shrimp Litopenaeus vannamei to a hazardous cyanotoxin nodularin exposure

Nodularin (NOD) is a harmful cyanotoxin that affects shrimp farming. The hepatopancreas and intestine of shrimp are the main target organs of cyanotoxins. In this study, we exposed Litopenaeus vannamei to NOD at 0.1 and 1 μg/L for 72 h, respectively, and changes in histology, oxidative stress, gene transcription, metabolism, and intestinal microbiota were investigated. After NOD exposure, the hepatopancreas and intestine showed obvious histopathological damage and elevated oxidative stress response. Transcription patterns of immune genes related to detoxification, prophenoloxidase and coagulation system were altered in the hepatopancreas. Furthermore, metabolic patterns, especially amino acid metabolism and arachidonic acid related metabolites, were also disturbed. The integration of differential genes and metabolites revealed that the functions of "alanine, aspartic acid and glutamate metabolism" and "aminoacyl-tRNA biosynthesis" were highly affected. Alternatively, NOD exposure induced the variation of the diversity and composition of intestinal microbiota, especially the abundance of potentially beneficial bacteria (Demequina, Phyllobacterium and Pseudoalteromonas) and pathogenic bacteria (Photobacterium and Vibrio). Several intestinal bacteria were correlated with the changes of host the metabolic function and immune factors. These results revealed the toxic effects of NOD on shrimp, and identified some biomarkers.

Joint role of land cover types and microbial processing on molecular composition of dissolved organic matter in inland lakes

Anthropogenic activities have greatly changed the land use and land cover (LULC) and further influenced the chemical properties and amount of DOM transported into aquatic systems, meanwhile, microbial processing is also critical to DOM molecular composition in freshwaters. However, how they jointly shape DOM's chemical composition and chemodiversity in lakes is poorly understood. Here we examined DOM characteristics for seven inland lakes with three different land cover conditions (forest-dominated, cropland-dominated, and urban-dominated). Results indicated that DOM in cropland-dominated and forest-dominated lakes exhibited more characteristics of terrestrial organic matter, while urban-dominated lakes had more allochthonous organic matter driven by relatively high nutrient input. Human activities extended terrestrial DOM input to lakes and intensified the amount of heteroatomic organic molecules containing nitrogen and sulfur in lakes, with cropland contributing more N-containing compounds and urban contributing more S-containing compounds. Differential bacterial community composition appeared in the three types of land cover lakes, while strong co-occurrence/exclusion patterns between specific microbes and molecular formula groups revealed the key DOM metabolism functions of these bacteria. Matrix correlations based on Mantel tests confirmed that watershed landcover status was a dominating factor for DOM sources and molecular composition in mountainous lakes through direct input of terrestrial organic matter, and microbial processing was not the key factor for DOM molecular formula. Our findings help to assess the influence of human activities and microbial processing in the transfer and transformation of DOM in environmental waters.

Effects of submerged macrophytes (Elodea nuttallii) on water quality and microbial communities of largemouth bass (Micropterus salmoides) ponds

Traditional aquaculture ponds are one of the most vulnerable ecosystems; thus, ecological aquaculture is increasingly valued for its beneficial ecological properties and ecosystem services. However, little is known about ecological aquaculture of largemouth bass with submerged vegetation. Here, we designed three ecological ponds of cultured largemouth bass with submerged macrophytes (the EM group) and three ponds with traditional aquaculture (the M group) to reveal the response of water quality, and phytoplankton and bacterial communities, to submerged macrophyte bioremediation during a 90-day culture period. We observed that Cyanobacterial outbreak occurred in the M group ponds from day 7 to the end of the experiment; however, there were no Cyanobacterial blooms in the EM group ponds throughout the culture period. Compared with the M group ponds, the EM group ponds, which had submerged hydrophytes, had significantly decreased concentrations of TP, TN, and COD_Mn, but significantly increased DO concentrations throughout the experimental period. Moreover, ecological aquaculture with submerged macrophytes showed strong effects on the phytoplankton and bacterial community compositions. In particular, the M group ponds had higher phytoplankton density and mainly included Cyanobacteria, whereas the EM group had lower phytoplankton density and mainly included Chlorophyta. Moreover, higher alpha diversity, as determined by Ace and Simpson index values, was detected for bacterial communities in the EM group ponds. Furthermore, PCoA clearly grouped the bacterial communities according to the two culture modes throughout the culture period. These results indicate that ecological aquaculture with submerged macrophytes can improve water quality, control Cyanobacterial blooms, and affect the diversity and composition of bacterial communities. These valuable effects seem to be beneficial and consistent to maintaining aquaculture ecosystem stability.

Linkages between the molecular composition of dissolved organic matter and soil microbial community in a boreal forest during freeze-thaw cycles

Soil dissolved organic matter (DOM) plays a vital role in biogeochemical processes. Global warming leads to increased freeze-thaw cycles (FTCs) in boreal forest soils, which can change DOM production and consumption. However, the interactions between the chemical composition of DOM molecules and the microbial communities that drive C decomposition in the context of freeze-thaw are poorly understood. Here, a FTCs incubation experiment was conducted. Combined with pyrolysis gas chromatography-mass spectrometry and high-throughput sequencing techniques, the relationships between DOM chemodiversity and microbial community structure were assessed. Results indicated that both low-frequency (2FTCs) and high-frequency freeze-thaw cycles (6FTCs) significantly increased soil dissolved organic carbon (DOC) contents in the surface (0-10 cm) and subsurface (50-60 cm) soil layers. In the topsoil, FTCs significantly reduced the relative abundance of aromatic compounds, but increased the relative proportions of alkanes, phenols, fatty acid methyl esters (Me) and polysaccharides in the DOM. In the subsuface soil layer, only the relative abundance of Me in the 6FTCs treatment increased significantly. The response of bacterial communities to FTCs was more sensitive than that of fungi, among which only the relative abundance of Gammaproteobacteria increased by FTCs. Moreover, the relative abundance of these taxa was positively correlated with the increment of DOC. Co-occurrence networks confirmed DOM-bacterial interactions, implying that specific microorganisms degrade specific substrates. At class level, Gammaproteobacteria were significantly positively correlated with labile C (polysaccharides and alkanes), whereas other bacterial classes such as Actinobacteria, Alphaproteobacteria, and Thermoleophilia were significantly positively correlated with aromatic compounds in the topsoil. Collectively, FTCs tended to activate DOM and enhance its biodegradability of DOM, potentially hampering DOC accumulation and C sequestration. These findings highlight the potential of DOM molecular mechanisms to regulate the functional states of soil bacterial communities under increased FTCs.

Bacterial response to glucose addition: growth and community structure in seawater microcosms from North Pacific Ocean

Onboard microcosm experiments were conducted to assess how bacterial growth pattern and community structure changed by the addition of labile organic compound during the KH-14-2 cruise of R/V Hakuho Maru (Atmosphere and Ocean Research Institute, the University of Tokyo and JAMSTEC) in May-June 2014. Seawater samples were collected from the three diversified oceanic environments, Kuroshio Current, North Pacific Sub-polar Gyre (SPG), and North Pacific Sub-tropical Gyre (STG) in the western North Pacific Ocean, filtered, supplemented with glucose, and incubated at 23 ± 1 °C, ~ 4 °C, and 23 ± 1 °C, respectively. Untreated control microcosms were also maintained for all the sample types. Significant increases in cell counts and cell sizes were observed in Kuroshio Current and STG waters, whereas in SPG neither the counts nor the sizes changed, even after 120 h of incubation. At early stages of incubation, the classes Bacteroidia, Alphaproteobacteria, and Gammaproteobacteria were dominant in the Kuroshio Current and SPG samples, while the phyla Cyanobacteria and Proteobacteria in the STG samples. Over incubation periods between 60 and 96 h, some members of the class Gammaproteobacteria gradually dominated within which the genera Vibrio and Alteromonas became dominant in the Kuroshio Current and STG, respectively. No growth was detected for the microcosms with seawater from SPG, regardless of glucose amendment. It is concluded that depending on the environmental condition, certain different bacterial groups proliferated quickly and modified the community structures. Temperature significantly influenced the growth and succession, and ultimately the community structure of bacteria.

Metabolite features of serum and intestinal microbiota response of largemouth bass (Micropterus salmoides) after Aeromonas hydrophila challenge

The enteric morphology, enteric microbiota structure and serum metabolomics of M. salmoides before and after infected by A. hydrophila were analysed to explore the pathogenic mechanism of A. hydrophila infection in M. salmoides. The results revealed that, after the infection of A. hydrophila, the villus boundary of largemouth bass became less obvious; the relative abundance of Proteobacteria and decreasing relative abundance of Tenericutes were increasing; genera relative abundance of putatively beneficial bacteria (Mycoplasma) were decreasing, whereas the genus Aeromonas increased after infection; serum metabolomic analysis showed that infection with A. hydrophila caused disorder to the metabolic processes of largemouth bass, particularly amino acid metabolism, and caused inflammation; several potential pathogen infection-related and significantly differential intestinal microbiota-related metabolite markers were identified, such as 6-hydroxy-5-methoxyindole glucuronide, zalcitabine, bilirubin, aciclovir. This study may provide new insights into the potential association between enteric microbiota and serum metabolism and the pathogenic mechanism of M. salmoides infected by A. hydrophila, providing a scientific basis for disease control in largemouth bass breeding.

You Exude What You Eat: How Carbon-, Nitrogen-, and Sulfur-Rich Organic Substrates Shape Microbial Community Composition and the Dissolved Organic Matter Pool

Phytoplankton is the major source of labile organic matter in the sunlit ocean, and they are therefore key players in most biogeochemical cycles. However, studies examining the heterotrophic bacterial cycling of specific phytoplankton-derived nitrogen (N)- and sulfur (S)-containing organic compounds are currently lacking at the molecular level. Therefore, the present study investigated how the addition of N-containing (glycine betaine [GBT]) and S-containing (dimethylsulfoniopropionate [DMSP]) organic compounds, as well as glucose, influenced the microbial production of new organic molecules and the microbial community composition. The chemical composition of microbial-produced dissolved organic matter (DOM) was analyzed by ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) demonstrating that CHO-, CHON-, and CHOS-containing molecules were enriched in the glucose, GBT, and DMSP experiments, respectively. High-throughput sequencing showed that Alteromonadales was the dominant group in the glucose, while Rhodobacterales was the most abundant group in both the GBT and DMSP experiments. Cooccurrence network analysis furthermore indicated more complex linkages between the microbial community and organic molecules in the GBT compared with the other two experiments. Our results shed light on how different microbial communities respond to distinct organic compounds and mediate the cycling of ecologically relevant compounds. IMPORTANCE Nitrogen (N)- and sulfur (S)-containing compounds are normally considered part of the labile organic matter pool that fuels heterotrophic bacterial activity in the ocean. Both glycine betaine (GBT) and dimethylsulfoniopropionate (DMSP) are representative N- and S-containing organic compounds, respectively, that are important phytoplankton cellular compounds. The present study therefore examined how the microbial community and the organic matter they produce are influenced by the addition of carbohydrate-containing (glucose), N-containing (GBT), and S-containing (DMSP) organic compounds. The results demonstrate that when these carbon-, N-, and S-rich compounds are added separately, the organic molecules produced by the bacteria growing on them are enriched in the same elements. Similarly, the microbial community composition was also distinct when different compounds were added as the substrate. Overall, this study demonstrates how the microbial communities metabolize and transform different substrates thereby, expanding our understanding of the complexity of links between microbes and substrates in the ocean.

Rapid Biotic and Abiotic Transformation of Toxins produced by Ostreopsis. cf. ovata

The dinoflagellate Ostreopsis cf. ovata produces several families of toxic polyketides. Despite only a few field measurements of these phycotoxins in seawater and aerosols, they are believed to be responsible for dermatitis and the toxic inhalations reported during blooms of this species. Therefore, the stability of these compounds in seawater is essential to understanding the causes of these symptoms, however, this has never been assessed. In the current study, the optimization of a solid phase extraction (SPE) procedure was first performed to ensure the most efficient extraction of all phycotoxins known to be produced by this strain, including the recently described liguriatoxins. The SPE cartridge SDBL® under non acidified conditions offered the best option. The stability of the ovatoxins and the liguriatoxins under biotic and abiotic stress was assessed by exposing the spent medium of a culture of Ostreopsis cf. ovata to its bacterial consortium and natural sunlight. A rapid biotic transformation was detected for both families of compounds. When exposed to bacteria, the half-lives of the ovatoxins were reached before 10 h and at 36 h, 97% of these toxins had been transformed. The half-lives of the liguriatoxins were 10 h under these conditions. Photolysis (abiotic degradation) of the ovatoxins (T1/2 < 36 h) was faster than for the liguriatoxins (T1/2 > 62 h). Although none of the catabolites of these phycotoxins were thoroughly identified, an untargeted metabolomics approach combined with molecular networking highlighted the presence of several compounds exhibiting structural similarities with the ovatoxins. Additional work should confirm the preliminary findings on these potential ovatoxins’ catabolites and their biological properties. The rapid transformation of O. cf. ovata’s phycotoxins introduces questions concerning their presence in seawater and their dispersion in the sea spray aerosols. The compounds involved in the toxic inhalations and dermatitis often experienced by beachgoers may stem from the catabolites of these toxins or even unrelated and as yet unidentified compounds.

Limited carbon cycling due to high-pressure effects on the deep-sea microbiome

Deep-sea microbial communities are exposed to high-pressure conditions, which has a variable impact on prokaryotes depending on whether they are piezophilic (that is, pressure-loving), piezotolerant or piezosensitive. While it has been suggested that elevated pressures lead to higher community-level metabolic rates, the response of these deep-sea microbial communities to the high-pressure conditions of the deep sea is poorly understood. Based on microbial activity measurements in the major oceanic basins using an in situ microbial incubator, we show that the bulk heterotrophic activity of prokaryotic communities becomes increasingly inhibited at higher hydrostatic pressure. At 4,000 m depth, the bulk heterotrophic prokaryotic activity under in situ hydrostatic pressure was about one-third of that measured in the same community at atmospheric pressure conditions. In the bathypelagic zone-between 1,000 and 4,000 m depth-~85% of the prokaryotic community was piezotolerant and ~5% of the prokaryotic community was piezophilic. Despite piezosensitive-like prokaryotes comprising only ~10% (mainly members of Bacteroidetes, Alteromonas) of the deep-sea prokaryotic community, the more than 100-fold metabolic activity increase of these piezosensitive prokaryotes upon depressurization leads to high apparent bulk metabolic activity. Overall, the heterotrophic prokaryotic activity in the deep sea is likely to be substantially lower than hitherto assumed, with major impacts on the oceanic carbon cycling.

Gramella sediminis sp. nov., isolated from a tidal flat of the Yellow Sea

A novel species of the genus Gramella , designated ASW11-100T, was isolated from a tidal flat sediment in the Yellow Sea, PR China. Phylogenetic analysis based on 16S rRNA gene sequences and single-copy orthologous clusters revealed that strain ASW11-100T belonged to the genus Gramella , and exhibited 16S rRNA gene sequence similarities of 98.9, 98.8 and 98.7 % to Gramella sabulilitoris HSMS-1T, Gramella sediminilitoris GHTF-27T and Gramella forsetii KT0803T, respectively. The genome of strain ASW11-100T harbours 2950 protein-coding genes and 105 carbohydrate-active enzymes including 38 glycoside hydrolases. Seventeen of the glycoside hydrolases are organized in five distinct polysaccharide utilization loci, which are predicted to involve in the degradation of starch, glucans, arabinoxylans, arabinomannan, arabinans and arabinogalactans. The genomic DNA G+C content was 37.3 mol%. The digital DNA–DNA hybridization and average nucleotide identity values between strain ASW11-100T and its closely related relatives were in ranges of 19.8–23.9% and 76.6–80.9 %, respectively. Cells of the isolate were Gram-negative, aerobic, non-flagellated and short rod-shaped. Carotenoid pigments were produced, but flexirubin-type pigments were absent. The major fatty acids (>10 %) were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1  ω6c and/or C16 : 1  ω7c). The sole respiratory quinone was menaquinone-6 and the major polar lipid was phosphatidylethanolamine. Based on the above polyphasic evidence, strain ASW11-100T should be considered to represent a novel Gramella species, for which the name Gramella sediminis sp. nov. is proposed. The type strain is ASW11-100T (=KCTC 82502T=MCCC 1K05580T).

Microbial ecology of the Southern Ocean

The Southern Ocean (SO) distributes climate signals and nutrients worldwide, playing a pivotal role in global carbon sequestration. Microbial communities are essential mediators of primary productivity and carbon sequestration, yet we lack a comprehensive understanding of microbial diversity and functionality in the SO. Here, we examine contemporary studies in this unique polar system, focusing on prokaryotic communities and their relationships with other trophic levels (i.e. phytoplankton and viruses). Strong seasonal variations and the characteristic features of this ocean are directly linked to community composition and ecosystem functions. Specifically, we discuss characteristics of SO microbial communities and emphasise differences from the Arctic Ocean microbiome. We highlight the importance of abundant bacteria in recycling photosynthetically derived organic matter. These heterotrophs appear to control carbon flux to higher trophic levels when light and iron availability favour primary production in spring and summer. Conversely, during winter, evidence suggests that chemolithoautotrophs contribute to prokaryotic production in Antarctic waters. We conclude by reviewing the effects of climate change on marine microbiota in the SO.

Salinimicrobium sediminilitoris sp. nov., Isolated from a Tidal Flat

A Gram-negative, facultatively anaerobic, motile, and rod-shaped bacterium, designated ASW11-47 ^T, was isolated from a tidal flat sediment taken from the coast of Qingdao, PR China. Phylogenetic analysis of 16S rRNA gene sequence showed that strain ASW11-47 ^T belongs to the genus Salinimicrobium and is most closely related to Salinimicrobium terrae YIM-C338^T (98.68% similarity). The length of draft genome is 3,594,457 bp, and DNA G + C content is 40.8 mol%. The values of average nucleotide identity and digital DNA-DNA hybridization between strain ASW11-47 ^T and closely related strains were in ranges of 75.9-85.9 and 19.7-31.5%, respectively. The major fatty acids (> 10%) were iso-C_15:0 and iso-C_17:0 3-OH. The predominant respiratory quinone was menaquinone-6 and the major polar lipid was phosphatidylethanolamine. On the basis of genotypic, phenotypic, and chemotaxonomic analysis, strain ASW11-47 ^T represents a novel species within the genus Salinimicrobium, for which the name Salinimicrobium sediminilitoris sp. nov. is proposed. The type strain is ASW11-47 ^T (= KCTC 82501 ^T = MCCC 1K05586^T).

Successful Application of Anammox Using the Hybrid Autotrophic-Heterotrophic Denitrification Process for Low-Strength Wastewater Treatment

Directly integrating anammox into sewage treatment is attractive, but anammox bacteria (AnAOB) enrichment is complex due to vicious competition from heterotrophic bacteria (HB). A novel strategy of optimal organics management using a preanaerobic stage and subsequent limited-oxygen conditions (0.32 ± 0.15 mg-O₂/L) is applied, and a hybrid autotrophic-heterotrophic denitrification process is developed to treat sewage-like wastewater with a COD/N ratio of 3.1 for 420 days. The stable process was achieved, and a high total nitrogen removal rate of 0.53 kg-N/(m³·d) was obtained compared to conventional nitrification/denitrification. The 16S rRNA high-throughput sequencing analysis suggested that the relative abundance of the nonendogenous HB (Denitratisoma and Thauera) was drastically reduced (P ≤ 0.001), whereas the endogenous denitrifying HB (Candidatus (Ca.) Competibacter) was significantly enriched in the anammox granules (9.98%, P ≤ 0.001). Moreover, Ca. Competibacter as an inner core and Nitrospira and Ca. Brocadia as an outside coating of the anammox granules indicated the cooperation of AnAOB with HB as revealed by laser-scanning confocal microscopy and qPCR. In situ tests further confirmed nitrite from two pathways (partial nitritation and endogenous partial denitritation) that favored AnAOB enrichment. Optimal organics management can mitigate the competition of HB with AnAOB by redirecting the metabolic pathways and microbial community, which is critical to directly integrating anammox into sewage treatment.

Dietary supplementation of two indigenous Bacillus spp on the intestinal morphology, intestinal immune barrier and intestinal microbial diversity of Rhynchocypris lagowskii

This study evaluated the effects of dietary administration of two indigenous Bacillus (A: basal control diet; B: 0.15 g/kg of Bacillus subtilis; C: 0.1 g/kg of Bacillus subtilis and 0.05 g/kg of Bacillus licheniformis; D: 0.05 g/kg of Bacillus subtilis and 0.1 g/kg of Bacillus licheniformis; E: 0.15 g/kg of Bacillus licheniformis) on the digestive enzyme activities, intestinal morphology, intestinal immune and barrier-related genes relative expression levels, and intestinal flora of Rhynchocypris lagowskii. The results showed that the fold height, lamina propria width, and muscle layer thickness of midgut and hindgut in group C were significantly higher than that of group A (P < 0.05). The activities of protease, amylase, and lipase in group C were significantly higher than those of group A (P < 0.05). The relative expression levels of IL-1β and IL-8 in the intestine of group C were significantly downregulated, and the relative expression levels of IL-10 and TGF-β were significantly upregulated (P < 0.05). The relative expression levels of Claudin-2 in group A significantly increased and the relative expression levels of Claudin-4 in group A significantly reduced compared with other groups (P < 0.05). The relative expression levels of ZO-1 in groups C and D were significantly higher than those of other groups (P < 0.05). The Bacillus in the intestine of group C has the highest relative abundance among all groups. Overall, it can generally be concluded that dietary supplementation of indigenous Bacillus subtilis and Bacillus licheniformis (group C) can improve the intestinal morphology, digestion, and absorption enzyme activities, enhance intestinal mucosal immunity and barrier function, and maintain the intestinal microbial balance of R. lagowskii.

Rapid bacterioplankton transcription cascades regulate organic matter utilization during phytoplankton bloom progression in a coastal upwelling system

Coastal upwelling zones are hotspots of oceanic productivity, driven by phytoplankton photosynthesis. Bacteria, in turn, grow on and are the principal remineralizers of dissolved organic matter (DOM) produced in aquatic ecosystems. However, the molecular processes that key bacterial taxa employ to regulate the turnover of phytoplankton-derived DOM are not well understood. We therefore carried out comparative time-series metatranscriptome analyses of bacterioplankton in the Northwest Iberian upwelling system, using parallel sampling of seawater and mesocosms with in situ-like conditions. The mesocosm experiment uncovered a taxon-specific progression of transcriptional responses from bloom development (characterized by a diverse set of taxa in the orders Cellvibrionales, Rhodobacterales, and Pelagibacterales), over early decay (mainly taxa in the Alteromonadales and Flavobacteriales), to senescence phases (Flavobacteriales and Saprospirales taxa). Pronounced order-specific differences in the transcription of glycoside hydrolases, peptidases, and transporters were found, supporting that functional resource partitioning is dynamically structured by temporal changes in available DOM. In addition, comparative analysis of mesocosm and field samples revealed a high degree of metabolic plasticity in the degradation and uptake of carbohydrates and nitrogen-rich compounds, suggesting these gene systems critically contribute to modulating the stoichiometry of the labile DOM pool. Our findings suggest that cascades of transcriptional responses in gene systems for the utilization of organic matter and nutrients largely shape the fate of organic matter on the time scales typical of upwelling-driven phytoplankton blooms.

Exploring bacterioplankton communities and their temporal dynamics in the rearing water of a biofloc-based shrimp (Litopenaeus vannamei) aquaculture system

Biofloc technology (BFT) has recently gained considerable attention as a sustainable method in shrimp aquaculture. In a successful BFT system, microbial communities are considered a crucial component in their ability to both improve water quality and control microbial pathogens. Yet, bacterioplankton diversity in rearing water and how bacterioplankton community composition changes with shrimp growth are rarely documented. In this study, the Pacific white shrimp, Litopenaeus vannamei was cultivated in a greenhouse-enclosed BFT system. Rearing water samples were collected on a weekly basis for 5 months (152 days) and water quality variables such as physicochemical parameters and inorganic nutrients were monitored. In parallel, 16S rRNA gene pyrosequencing was employed to investigate the temporal patterns of rearing-water microbiota. The productivity, survival rate, and feed conversion ratio were 3.2-4.4 kg/m3, 74%-89%, and 1.2-1.3, respectively, representing successful super-intensive cultures. The metataxonomic results indicated a highly dynamic bacterioplankton community, with two major shifts over the culture. Members of the phylum Planctomycetes dominated in rearing water during the early stages, while Actinobacteria dominated during the middle stages, and Chloroflexi and TM7 dominated during the late stages of culture. The bacterioplankton community fluctuated more in the beginning but stabilized as the culture progressed. Intriguingly, we observed that certain bacterioplankton groups dominated in a culture-stage-specific manner; these groups include Rhodobacteraceae, Flavobacteriaceae, Actinobacteria, and Chloroflexi, which either contribute to water quality regulation or possess probiotic potential. Altogether, our results indicate that an operationally successful BFT-based aquaculture system favors the growth and dynamics of specific microbial communities in rearing water. Our study expands the scientific understanding of the practical utilization of microbes in sustainable aquaculture. A thorough understanding of rearing-water microbiota and factors influencing their dynamics will help to establish effective management strategies.

The role of attached bacteria in the formation of Microcystis colony in Chentaizi River

To further understand the role of attached bacteria in the formation of Microcystis colonies, we conducted a field investigation in Chentaizi River in Tianjin, China, which frequently suffers Microcystis blooms in summer. The results showed the average cell density of Microcystis was 2.31 × 10⁷ cell/L from July 19 to July 27, 2021. Free-living and attached bacteria communities shared similar phylum diversity, but the abundance changed obviously. The colony size of Microcystis and attached bacterial number in the colony showed an increasing trend during the whole sampling period. There was a significant positive correlation between Microcystis colonial size and attached bacterial density (P < 0.01), indicating attached bacteria could contribute the colony formation of Microcystis. The genus composition in attached bacterial community varied in colonies of different sizes. The relative abundance of Acinetobacter, Cloacibacterium, Sphingobacterium, and Ralstonia in >90 μm colonies were significantly higher than those in 8-20 μm and 20-90 μm colonies (P < 0.05). These genera might have positive effects on the colony formation of Microcystis during sampling.

Structure and activity of marine bacterial communities responding to plastic leachates

Plastic in the ocean releases organic compounds that are able to enter the marine dissolved organic carbon pool and be utilized by heterotrophic bacteria. However, no information is known about which groups of bacteria are able to grow and degrade plastic leachates. Here we characterized a marine bacterial community from the NW Mediterranean Sea growing on plastic leachates and quantified its total activity. We used two petro-based plastics, low density polyethylene (LDPE) and polystyrene, and one biodegradable plastic, polylactic acid (PLA), to generate leachates under irradiated (UV-Vis) and non-irradiated conditions. Then we incubated them with a natural bacterial inoculum and determined the single-cell activity and associated taxonomy of the bacterial groups, using a combination of Catalyzed Reporter Deposition-Fluorescence In Situ Hybridization (CARDFISH) and BioOrthogonal Non-Canonical Amino acid Tagging (BONCAT). The community growing in the leachates was mainly composed of Alteromonas (Gammaproteobacteria), followed by Roseobacter (Alphaproteobacteria) and unclassified Gammaproteobacteria. Overall, marine bacteria in the irradiated treatments showed higher total activity compared to the non-irradiated ones, with the community growing on LDPE's leachates presenting the highest values. The biodegradable PLA leachates presented lower activity than those from petro-based plastics but similar bacterial composition, suggesting that it is possible that PLA could last in the ocean as much as petro-based plastics do. The results from this study show the impact of marine plastic debris in the marine microbial community and the marine carbon cycle.

Deep ocean microbial communities produce more stable dissolved organic matter through the succession of rare prokaryotes

The microbial carbon pump (MCP) hypothesis suggests that successive transformation of labile dissolved organic carbon (DOC) by prokaryotes produces refractory DOC (RDOC) and contributes to the long-term stability of the deep ocean DOC reservoir. We tested the MCP by exposing surface water from a deep convective region of the ocean to epipelagic, mesopelagic, and bathypelagic prokaryotic communities and tracked changes in dissolved organic matter concentration, composition, and prokaryotic taxa over time. Prokaryotic taxa from the deep ocean were more efficient at consuming DOC and producing RDOC as evidenced by greater abundance of highly oxygenated molecules and fluorescent components associated with recalcitrant molecules. This first empirical evidence of the MCP in natural waters shows that carbon sequestration is more efficient in deeper waters and suggests that the higher diversity of prokaryotes from the rare biosphere holds a greater metabolic potential in creating these stable dissolved organic compounds.

Effects of alder- and salmon-derived nutrients on aquatic bacterial community structure and microbial community metabolism in subarctic lakes

Alder (Alnus spp.) and Pacific salmon (Oncorhynchus spp.) provide key nutrient subsidies to freshwater systems. In southwestern Alaska, alder-derived nutrients (ADNs) are increasing as alder cover expands in response to climate warming, while climate change and habitat degradation are reducing marine-derived nutrients (MDNs) in salmon-spawning habitats. To assess the relative influences of ADN and MDN on aquatic microbial community structure and function, we analyzed lake chemistry, bacterial community structure, and microbial metabolism in 13 lakes with varying alder cover and salmon abundance in southwestern Alaska. We conducted bioassays to determine microbial nutrient limitation and physical factors modulating microbial response to nutrient inputs (+N, +P and +NP treatments). Seasonal shifts in bacterial community structure (F = 7.47, P < 0.01) coincided with changes in lake nitrogen (N) and phosphorus (P) concentrations (r² = 0.19 and 0.16, both P < 0.05), and putrescine degradation (r² = 0.13, P = 0.06), suggesting the influx and microbial use of MDN. Higher microbial metabolism occurred in summer than spring, coinciding with salmon runs. Increased microbial metabolism occurred in lakes where more salmon spawned. Microbial metabolic activity was unrelated to alder cover, likely because ADN provides less resource diversity than MDN. When nutrients were added to spring samples, there was greater substrate use by microbial communities from lakes with elevated Chl a concentrations and large relative catchment areas (β estimates for all treatments > 0.56, all P < 0.07). Thus, physical watershed and lake features mediate the effects of nutrient subsidies on aquatic microbial metabolic activity.

Temporal heterogeneity of bacterial communities and their responses to Raphidiopsis raciborskii blooms

To elucidate the interspecies connectivity between cyanobacteria and other bacteria (noncyanobacteria), microbial diversity and composition were investigated through high-throughput sequencing (HTS) in a drinking water reservoir in Chongqing city, Southwest China, during Raphidiopsis raciborskii blooms. Significant temporal changes were observed in microbial community composition during the sampling period, primarily reflected by variations in relative bacterial abundance. The modularity analysis of the network demonstrated that the bacterial community forms co-occurrence/exclusion patterns in response to variations in environmental factors. Moreover, five modules involved in the dynamic phases of the R. raciborskii bloom were categorized into the Pre-Bloom, Bloom, Post-Bloom, and Non-Bloom Groups. The reservoir was eutrophic (i.e., the average concentrations of total nitrogen (TN) and total phosphorus (TP) were 2.32 and 0.07 mg L^-1, respectively) during the investigation; however, Pearson's correlation coefficient showed that R. raciborskii was not significantly correlated with nitrogen and phosphorus. However, other environmental factors, such as water temperature, pH, and the permanganate index, were positively correlated with R. raciborskii. Importantly, Proteobacteria (α-, γ-Proteobacteria), Acidobacteria, Chloroflexi, and Firmicutes were preferentially associated with increased R. raciborskii blooms. These results suggested that the transition of R. raciborskii bloom-related microbial modules and their keystone species could be crucial in the development and collapse of R. raciborskii blooms and could provide a fundamental basis for understanding the linkage between the structure and function of the microbial community during bloom dynamics.

Microbial Community Composition of the Antarctic Ecosystems: Review of the Bacteria, Fungi, and Archaea Identified through an NGS-Based Metagenomics Approach

Antarctica represents a unique environment, both due to the extreme meteorological and geological conditions that govern it and the relative isolation from human influences that have kept its environment largely undisturbed. However, recent trends in climate change dictate an unavoidable change in the global biodiversity as a whole, and pristine environments, such as Antarctica, allow us to study and monitor more closely the effects of the human impact. Additionally, due to its inaccessibility, Antarctica contains a plethora of yet uncultured and unidentified microorganisms with great potential for useful biological activities and production of metabolites, such as novel antibiotics, proteins, pigments, etc. In recent years, amplicon-based next-generation sequencing (NGS) has allowed for a fast and thorough examination of microbial communities to accelerate the efforts of unknown species identification. For these reasons, in this review, we present an overview of the archaea, bacteria, and fungi present on the Antarctic continent and the surrounding area (maritime Antarctica, sub-Antarctica, Southern Sea, etc.) that have recently been identified using amplicon-based NGS methods.

Characteristics, Biodiversity, and Cultivation Strategy of Low Nucleic Acid Content Bacteria

Low nucleic acid content (LNA) bacteria are ubiquitous and estimated to constitute 20%–90% of the total bacterial community in marine and freshwater environment. LNA bacteria with unique physiological characteristics, including small cell size and small genomes, can pass through 0.45-μm filtration. The researchers came up with different terminologies for low nucleic acid content bacteria based on different research backgrounds, such as: filterable bacteria, oligotrophic bacteria, and low-DNA bacteria. LNA bacteria have an extremely high level of genetic diversity and play an important role in material circulation in oligotrophic environment. However, the majority of LNA bacteria in the environment remain uncultivated. Thus, an important challenge now is to isolate more LNA bacteria from oligotrophic environments and gain insights into their unique metabolic mechanisms and ecological functions. Here, we reviewed LNA bacteria in aquatic environments, focusing on their characteristics, community structure and diversity, functions, and cultivation strategies. Exciting future prospects for LNA bacteria are also discussed.

Asymmetry Evaluation of Sea Cucumber (Apostichopus japonicus) Gut and Its Surrounding Environment in the Bacterial Community

Animals are not only regulated by their own genes but also influenced by symbiotic bacteria, most of which are colonized in the gut. The gut bacterial community is involved in plenty of physiological processes; therefore, intestinal colonization by commensal microbiota is essential to the health of the host animal. Here, metagenome sequencing of the A. japonicus gut, surrounding water, and feed was performed to explore the structural and functional characteristics of the colonized bacteria in the gut of A. japonicus. Results showed that Bacteroidetes and Proteobacteria were the main dominant phyla of the A. japonicus gut, and Formosa, Vibrio, and Lactobacillus were the dominant genera. There was asymmetry between the A. japonicus gut and its surrounding environment in the bacterial community. In terms of the top 50 abundant genera, those colonized in the gut shared a similarity of 26% with those colonized in the surrounding water and a similarity of 30% with those colonized in the feed. According to KEGG annotation, the dominant metabolic pathways in the gut of A. japonicus were glycan biosynthesis and metabolism, nitrogen metabolism, and cysteine and methionine metabolism. This implies that the gut-colonized bacteria of A. japonicus are influenced by the surrounding water and the feed. In addition, the gut-colonized bacteria might be related to the growth and metabolism of A. japonicus.

Analysis of antibiotic resistance genes reveals their important roles in influencing the community structure of ocean microbiome

Antibiotic resistance gene (ARG) content is a well-established driver of microbial abundance and diversity in an environment. By reanalyzing 132 metagenomic datasets from the Tara Oceans project, we aim to unveil the associations between environmental factors, the ocean microbial community structure and ARG contents. We first investigated the structural patterns of microbial communities including both prokaryotes such as bacteria and eukaryotes such as protists. Additionally, several ARG-dominant horizontal gene transfer events between Protist and Prokaryote have been identified, indicating the potential roles of ARG in shaping the ocean microbial communities. For a deeper insight into the role of ARGs in ocean microbial communities on a global scale, we identified 1926 unique types of ARGs and discovered that the ARGs are more abundant and diverse in the mesopelagic zone than other water layers, potentially caused by limited resources. Finally, we found that ARG-enriched genera were often more abundant compared to their ARG-less neighbors in the same environment (e.g. coastal oceans). A deeper understanding of the ARG-microbiome relationships could help in the conservation of the oceanic ecosystem.