Influence of short and long term processes on SAR11 communities in open ocean and coastal systems

Alterations in bacterial structure and function in seawater due to Mytilus coruscus farming: implications for sustainable aquaculture management

Microorganisms are essential for maintaining the ecological balance and supporting the health of aquatic animals in aquaculture environments. This study utilized high-throughput sequencing technology to analyze the diversity, composition, co-occurrence networks, assembly mechanisms, and functional predictions of bacterial communities in seawater from both Mytilus coruscus aquaculture areas (AA) and non-aquaculture areas (NAA) across different seasons. The results indicated that the number of operational taxonomic units (OTUs) in the AA group was higher than the NAA group, while the Simpson index was significantly lower in the bottom water (p < 0.05). Additionally, the β-diversity (Bray-Curtis distance and βMNTD) was significantly reduced in the AA group compared to the NAA group (p < 0.05). M. coruscus farming influenced the relative abundance of certain genera, including Pseudoalteromonas, HIMB11, and Clade Ia, with the AA group exhibiting a greater number of specialist species. Co-occurrence network analysis revealed that the bacterial network in the NAA group had a higher number of nodes, edges, and modularity, whereas the AA group displayed greater closeness centrality and betweenness centrality. Following the removal of 80% of the nodes, the natural connectivity of the surface water in the AA group declined more rapidly than in the NAA group. Homogeneous selection was the primary assembly mechanism of bacterial communities in the AA group, while diffusion limitation was predominant in the NAA group. FAPROTAX functional predictions indicated the higher relative abundance of functions associated with organic matter degradation and nitrogen cycling in the AA group. These findings suggest that M. coruscus farming activities significantly alter the structure and function of bacterial communities in seawater, providing valuable data to support sustainable aquaculture for M. coruscus and optimize fisheries' carbon sink management strategies.

Seasonal dynamics and factors shaping microbiomes in freshwater finfish earthen aquaculture ponds in Bangladesh

BACKGROUND

The pondwater microbiome is believed to play a key role in fish health, including shaping mucosal surface microbiomes that help to protect against disease. How different physiochemical features relating to season, geographical locations, as well as crop species shape the pond water microbiome in the finfish aquaculture system, is not well established. Pangasius (Pangasianodon hypophthalmus) and tilapia (Oreochromis niloticus) are two of the most widely farmed fish species and disease is a major impediment to the expansion of their production. We applied 16S and 18S rRNA metabarcoding to assess how pond physicochemistry and geographical location shape water microbiomes in pangasius and tilapia aquaculture earthen ponds in Bangladesh.

RESULTS

Planctomycetota, Pseudomonadota and Actinomycetota were the dominant bacterial phyla while Stramenopiles and Alveolata were the dominant microeukaryotes (divisions) in the pangasius and tilapia ponds water. The relative abundance of Planctomycetota was higher in the pangasius ponds compared with tilapia ponds, and Actinomycetota, and Pseudomonadota were relatively higher in tilapia ponds. Tilapia pond water also exhibited a higher microbial diversity compared to that in pangasius ponds. The pondwater microbial diversity was at its lowest in winter (and/or in monsoon) and highest in the pre-monsoon period. The microbial community structures differed across the different seasons, geographical locations, culture systems, and crop species, with season and geographical locations showing the strongest effects. Of the water physicochemistry features assessed, temperature and pH were found to have a weak but significant effect on the water microbiome content for both pangasius and tilapia ponds. Pangasius and tilapia ponds shared over 46% of ASVs, and around 30% of ASVs were shared across the different study geographical locations.

CONCLUSION

Our findings demonstrate that microbial communities in pangasius and tilapia aquaculture systems in Bangladesh are shaped by season, geographical location, crop species, as well as effects from water physicochemistry. Our results provide insights into the dynamic nature and environmental influences on water microbiomes that may be applied for use in pond management for improving aquaculture productivity and enhancement of overall fish health.

Comparative analysis of crab growth performance, enzyme activity, and microbiota between rice-crab coculture and pond farming systems

Introduction

To support the sustainable development of rice and aquaculture industries, various rice-animal coculture systems have been developed. One such system, the rice-crab coculture system (RCC), has been practiced for decades in northern China. However, studies on the crab physiological status in RCC remain limited. Microorganisms play a crucial role in aquaculture by influencing animal nutrition, health, nutrient cycling, water quality, and environmental impact. Research on the gut and environmental microbiota in RCC is scarce.

Methods

This study compared the growth performance, immune and digestive enzyme activities of crabs between RCC and traditional pond farming system (PF). In addition, the microbiota in crab guts, water, and sediment from both systems was investigated using 16S rRNA gene sequencing.

Results

Crabs in RCC exhibited superior growth performance and higher enzymatic activities, including acid phosphatase (ACP), alkaline phosphatase (AKP), lipase (LPS), and trypsin (TRY). Significant differences were observed in microbiota composition across crab gut, water, and sediment samples, respectively. RCC crabs had a lower abundance of Bacteroidota and a higher abundance of Firmicutes in their gut microbiota. The RCC environment was enriched with beneficial bacteria such as Rhizobiales, Methylococcales, KD4-96, C39, Xanthomonadales, and Nitrosomonadaceae. Microbial function predictions confirmed enhanced methanotrophy and nitrogen fixation in the RCC.

Discussion

The RCC enhances the growth rate and immune capability of crabs. Crabs from RCC consume more animal-based nutrition, which results in distinct differences in gut microbiota composition and higher levels of LPS and TRY compared to those in PF. Additionally, RCC supports environmentally beneficial bacteria that contribute to greenhouse gas reduction, carbon and nitrogen fixation, organic matter decomposition, and ammonia oxidation, benefiting both the crabs and their ecosystem. These findings enhance our understanding of crab physiology and microbial communities in RCC and PF systems.

Large diversity in the O-chain biosynthetic cluster within populations of Pelagibacterales

Genomic diversity in prokaryotic species is largely due to the existence of extensive pangenomes, allowing different gene complements to be drawn depending on the strain. Here, we have studied the diversity of the O-chain polysaccharide biosynthesis cluster (OBC) in marine bacteria of the Pelagibacterales order as a proxy to measure such genetic diversity in a single population. The study of single-amplified genomes (SAGs) from the whole order found a pattern similar to that of other well-studied microbes, such as the Enterobacteriales or Alteromonas, where distinct OBCs represent strains containing different gene pools. We found that most of the OBC sharing happened among individuals of the same clonal frame (>99% average nucleotide identity). Moreover, given the parsimonious way this cluster changes, the diversity of the OBCs can be extrapolated to the size of the population's pangenome. This assumes that different OBCs correspond to lineages containing unique flexible gene pools, as seen in the aforementioned microbes. Through long-read metagenomics, we could detect 380 different OBCs at a single Mediterranean sampling site. Within a single population (single species and sample) of the endemic Ia.3/VII (gMED) genomospecies, we identified 158 OBCs, of which 130 were unique. These findings suggest that the gene pool within a single population might be substantial (several thousands). While this figure is large, it aligns with the complexity of the dissolved organic matter that these organisms can potentially degrade.IMPORTANCEDifferent strains of the same bacterial species contain very different gene pools. This has been long known by epidemiologists. However, it is unknown what gene pool is present in a single set of environmental conditions, i.e., the same time and place in free-living bacteria. Here, we have leveraged information from SAGs to analyze the diversity of the gene cluster coding for the O-chain polysaccharide, a typical component of the flexible gene pool classically used as a tool to differentiate strains in clinical microbiology. It evolves at a similar rate to the rest of the genome and does not seem to be affected by an arms race with phages. One single species of Pelagibacteriales (gMED) revealed an astounding diversity in one sample studied by long-read metagenomics. Our results point to a large gene pool (local pangenome) present in a single population, which is critical to interpreting the biological meaning of the pangenome, i.e., it provides intrapopulation diversity rather than characterizing strains with different distribution in time and/or space.

The assembly and ecological roles of biofilms attached to plastic debris of Ashmore reef

Plastic pollution in the ocean is a global environmental hazard aggravated by poor management of plastic waste and growth of annual plastic consumption. Microbial communities colonizing the plastic's surface, the plastisphere, has gained global interest resulting in numerous efforts to characterize the plastisphere. However, there are insufficient studies deciphering the underlying metabolic processes governing the function of the plastisphere and the plastic they reside upon. Here, we collected plastic and seawater samples from Ashmore Reef in Australia to examine the planktonic microbes and plastic associated biofilm (PAB) to investigate the ecological impact, pathogenic potential, and plastic degradation capabilities of PAB in Ashmore Reef, as well as the role and impact of bacteriophages on PAB. Using high-throughput metagenomic sequencing, we demonstrated distinct microbial communities between seawater and PAB. Similar numbers of pathogenic bacteria were found in both sample types, yet plastic and seawater select for different pathogen populations. Virulence Factor analysis further illustrated stronger pathogenic potential in PAB, highlighting the pathogenicity of environmental PAB. Furthermore, functional analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways revealed xenobiotic degradation and fatty acid degradation to be enriched in PABs. In addition, construction of metagenome-assembled genomes (MAG) and functional analysis further demonstrated the presence of a complete Polyethylene (PE) degradation pathway in multiple Proteobacteria MAGs, especially in Rhodobacteriaceae sp. Additionally, we identified viral population presence in PAB, revealing the key role of bacteriophages in shaping these communities within the PAB. Our result provides a comprehensive overview of the various ecological processes shaping microbial community on marine plastic debris.

Gradients of bacteria in the oceanic water column reveal finely-resolved vertical distributions

Bacterial communities directly influence ecological processes in the ocean, and depth has a major influence due to the changeover in primary energy sources between the sunlit photic zone and dark ocean. Here, we examine the abundance and diversity of bacteria in Monterey Bay depth profiles collected from the surface to just above the sediments (e.g., 2000 m). Bacterial abundance in these Pacific Ocean samples decreased by >1 order of magnitude, from 1.22 ±0.69 ×106 cells ml-1 in the variable photic zone to 1.44 ± 0.25 ×105 and 6.71 ± 1.23 ×104 cells ml-1 in the mesopelagic and bathypelagic, respectively. V1-V2 16S rRNA gene profiling showed diversity increased sharply between the photic and mesopelagic zones. Weighted Gene Correlation Network Analysis clustered co-occurring bacterial amplicon sequence variants (ASVs) into seven subnetwork modules, of which five strongly correlated with depth-related factors. Within surface-associated modules there was a clear distinction between a 'copiotrophic' module, correlating with chlorophyll and dominated by e.g., Flavobacteriales and Rhodobacteraceae, and an 'oligotrophic' module dominated by diverse Oceanospirillales (such as uncultured JL-ETNP-Y6, SAR86) and Pelagibacterales. Phylogenetic reconstructions of Pelagibacterales and SAR324 using full-length 16S rRNA gene data revealed several additional subclades, expanding known microdiversity within these abundant lineages, including new Pelagibacterales subclades Ia.B, Id, and IIc, which comprised 4-10% of amplicons depending on the subclade and depth zone. SAR324 and Oceanospirillales dominated in the mesopelagic, with SAR324 clade II exhibiting its highest relative abundances (17±4%) in the lower mesopelagic (300-750 m). The two newly-identified SAR324 clades showed highest relative abundances in the photic zone (clade III), while clade IV was extremely low in relative abundance, but present across dark ocean depths. Hierarchical clustering placed microbial communities from 900 m samples with those from the bathypelagic, where Marinimicrobia was distinctively relatively abundant. The patterns resolved herein, through high resolution and statistical replication, establish baselines for marine bacterial abundance and taxonomic distributions across the Monterey Bay water column, against which future change can be assessed.

Metagenomic time series reveals a Western English Channel viral community dominated by members with strong seasonal signals

Marine viruses are key players of ocean biogeochemistry, profoundly influencing microbial community ecology and evolution. Despite their importance, few studies have explored continuous inter-seasonal viral metagenomic time series in marine environments. Viral dynamics are complex, influenced by multiple factors such as host population dynamics and environmental conditions. To disentangle the complexity of viral communities, we developed an unsupervised machine learning framework to classify viral contigs into "chronotypes" based on temporal abundance patterns. Analysing an inter-seasonal monthly time series of surface viral metagenomes from the Western English Channel, we identified chronotypes and compared their functional and evolutionary profiles. Results revealed a consistent annual cycle with steep compositional changes from winter to summer and steadier transitions from summer to winter. Seasonal chronotypes were enriched in potential auxiliary metabolic genes of the ferrochelatases and 2OG-Fe(II) oxygenase orthologous groups compared to non-seasonal types. Chronotypes clustered into four groups based on their correlation profiles with environmental parameters, primarily driven by temperature and nutrients. Viral contigs exhibited a rapid turnover of polymorphisms, akin to Red Queen dynamics. However, within seasonal chronotypes, some sequences exhibited annual polymorphism recurrence, suggesting that a fraction of the seasonal viral populations evolve more slowly. Classification into chronotypes revealed viral genomic signatures linked to temporal patterns, likely reflecting metabolic adaptations to environmental fluctuations and host dynamics. This novel framework enables the identification of long-term trends in viral composition, environmental influences on genomic structure, and potential viral interactions.

Novel pelagiphage isolate Polarivirus skadi is a polar specialist that dominates SAR11-associated bacteriophage communities at high latitudes

The SAR11 clade are the most abundant members of surface marine bacterioplankton and a critical component of global biogeochemical cycles. Similarly, pelagiphages that infect SAR11 are ubiquitous and highly abundant in the oceans. Pelagiphages are predicted to shape SAR11 community structures and increase carbon turnover throughout the oceans. Yet, ecological drivers of host and niche specificity of pelagiphage populations are poorly understood. Here we report the global distribution of a novel pelagiphage called "Polarivirus skadi", which is the sole representative of a novel genus. P. skadi was isolated from the Western English Channel using a cold-water ecotype of SAR11 as bait. P. skadi is closely related to the globally dominant pelagiphage HTVC010P. Along with other HTVC010P-type viruses, P. skadi belongs to a distinct viral family within the order Caudovirales, for which we propose the name Ubiqueviridae. Metagenomic read recruitment identified P. skadi as one of the most abundant pelagiphages on Earth. P. skadi is a polar specialist, replacing HTVC010P at high latitudes. Experimental evaluation of P. skadi host range against cold- and warm-water SAR11 ecotypes supported cold-water specialism. Relative abundance of P. skadi in marine metagenomes correlated negatively with temperature, and positively with nutrients, available oxygen, and chlorophyll concentrations. In contrast, relative abundance of HTVC010P correlated negatively with oxygen and positively with salinity, with no significant correlation to temperature. The majority of other pelagiphages were scarce in most marine provinces, with a few representatives constrained to discrete ecological niches. Our results suggest that pelagiphage populations persist within a global viral seed bank, with environmental parameters and host availability selecting for a few ecotypes that dominate ocean viromes.