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Cold seeps are biological oases of the deep sea fueled by methane, sulfates, nitrates, and other inorganic sources of energy. Chemolithoautotrophic bacteria and archaea dominate seep sediment, and their diversity and biogeochemical functions are well established. Fungi are likewise diverse, metabolically versatile, and known for their ability to capture and oxidize methane. Still, no study has ever explored the functional role of the mycobiota in the cold seep biome. To assess the complex role of fungi and fill in the gaps, we performed network analysis on 147 samples to disentangle fungal-prokaryotic interactions (fungal 18S and prokaryotic 16S) in the Haima cold seep region. We demonstrated that fungi are central species with high connectivity at the epicenter of prokaryotic networks, reduce their random-attack vulnerability by 60%, and enhance information transfer efficiency by 15%. We then scavenged a global metagenomic and metatranscriptomic data set from 10 cold seep regions for fungal genes of interest (hydrophobins, cytochrome P450s, and ligninolytic family of enzymes); this is the first study to report active transcription of 2,5001 fungal genes in the cold seep sediment. The genera Fusarium and Moniliella were of notable importance and directly correlated with high methane abundance in the sulfate-methane transition zone (SMTZ), likely due to their ability to degrade and solubilize methane and oils. Overall, our results highlight the essential yet overlooked contribution of fungi to cold seep biological networks and the role of fungi in regulating cold seep biogeochemistry.

Nutrient pollution in the coastal environment has been accelerated by progressively intensifying aquaculture activities. Excessive nutrients can lead to coastal eutrophication with serious economic and ecological consequences. In this study, we studied coastal planktonic microbial community over a year to understand the aquaculture impact on coastal water quality and function. We observed increased total inorganic nitrogen concentrations in active fish farms to favor the diverse Alpha- and Gammaproteobacteria. Bacterial community alpha diversity in fish farms was positively correlated with total inorganic nitrogen, and active fish farming co-influenced the bacterial structural composition and regional beta diversity. By analyzing the nitrogen cycle-related functional compositions and pathways using PICRUSt2 prediction on inferred genomes, we identified the contribution of over 600 bacterial species to four major pathways. Enhanced nitrogen load in active fish farms was positively correlated with elevated dissimilatory nitrate reduction and denitrification pathway abundances. Fallowed fish farms were characterized by a predicted high abundance of nirA and narB genes contributing to assimilatory nitrate reduction pathway due to the prevalence of Cyanobacteria. Overall, these results suggested active operation and short hiatus in coastal aquaculture practices could rapidly impact planktonic bacterial communities and further influence nitrogen cycling and associated processes. These findings will improve the understanding of the responses and interactions between microbiome and aquaculture activities. In a world of increasing aquaculture demands, this work has important implications for sustainable water resource management and development. Copyright © 2022 Lo, Xu, Lee, Lau, Qiu, Liu, Qian and Cheng.

Mesoscale eddies are ubiquitous oceanographic features that influence the metabolism and community structure of Synechococcus. However, the metabolic adaptations of this genus to eddy-associated environmental changes have rarely been studied. We recovered two high-quality Synechococcus metagenome-assembled genomes (MAGs) from eddies in the South China Sea and compared their metabolic variations using metatranscriptomic samples obtained at the same time. The two MAGs (syn-bin1 and syn-bin2) are affiliated with marine Synechococcus subclusters 5.2 (S5.2) and 5.3 (S5.3), respectively. The former exhibited a higher abundance at the surface layer, whereas the latter was more abundant in the deep euphotic layer. Further analysis indicated that syn-bin1 had a strong ability to utilize organic nutrients, which could help it to thrive in the nutrient-deprived surface water. By contrast, syn-bin2 had the genetic potential to perform chromatic acclimation, which could allow it to capture green or blue light at different depths. Additionally, transcriptomic analysis showed that syn-bin2 upregulated genes involved in the synthesis of C4 acids, photosystem II proteins, and (Formula presented.) transporters in the deep euphotic layer, which might contribute to its predominance in low-light environments. Overall, this study expands our understanding of oceanic S5.2 and S5.3 Synechococcus by revealing their metabolic adaptations to mesoscale eddies.

Microeukaryotes are diverse with different trophic modes and play important roles in many habitats. Same to other microorganisms, their communities are fundamentally affected by several deterministic (e.g., environmental selection) and stochastic (e.g., ecological drift) processes. How this suite of different processes regulates the biogeography of microeukaryotes remains to be comprehensively explored. In this thesis, microeukaryotic community and its regulating ecological processes were explored at different habitats including coastal, pelagic ocean and cold seep sediment. The results showed that (1) heterogeneous selection mainly regulated the phytoplankton (both eukaryotic and prokaryotic) communities in the Pacific Ocean, with varying relative importance (compared with other processes) across spaces due to the spatial scale, traits of phytoplankton and environmental gradients; (2) Ocean current, by promoting species dispersal, played important roles in the connectivity between local microeukaryotic communities in coastal regions. It largely homogenized the community (by homogenizing dispersal) and reduced the effects of environmental selection, leading to the weak relations between community composition and measured environmental factors; (3) Microeukaryotic communities in the cold seep sediment, represented by abundant and diverse parasitic taxa, were regionally divergent with local phylogenesis. Relative higher species dispersal rate and heterogeneous selection (mainly from metazoans) made active cold seep as hotspots for microeukaryotic diversity. These mechanistic findings deepen our understanding of community ecology of microeukaryotes and provide indications for conservations of marine biodiversity.

1. Effects of nutrient-imbalanced diet on the growth and fitness of zooplankton were widely reported as key issues to aquatic ecology. However, little is known about the molecular mechanisms driving the physiological changes of zooplankton under nutrient stress. 2. In this study, we investigated the physiological fitness and transcriptomic response of Daphnia magna when exposed to nitrogen (N)-limited or phosphorus (P)-limited algal diet (Chlamydomonas reinhardtii) compared to regular algae (N and P saturated). 3. D. magna showed higher ingestion rates and overexpression of genes encoding digestive enzymes when fed with either N-limited or P-limited algae, reflecting the compensatory feeding. Under P-limitation, both growth rate and reproduction rate of D. magna were greatly reduced, which could be attributed to the downregulated genes within the pathways of cell cycle and DNA replication. Growth rate of D. magna under N-limitation was similar to normal group, which could be explained by the high methylation level (by degradation of methionine) supporting the body development. 4. Phenotypic changes of D. magna under nutrient stress were explained by gene and pathway regulations from transcriptome data. Generally, D. magna invested more on growth under N-limitation but kept maintenance (e.g., cell structure and defense to external stress) in priority under P-limitation. Post-translational modifications (e.g., methylation and protein folding) were important for D. magna to deal with nutrient constrains. 5. This study reveals the fundamental mechanisms of zooplankton in dealing with elemental imbalanced diet and sheds light on the transfer of energy and nutrient in aquatic ecosystems

Aim: In microbial biogeography, it is crucial to link spatial patterns with underlying drivers in natural ecosystems. Bacterial communities driving key biogeochemical processes in coastal zones, which are important interfaces between terrestrial and marine ecosystems, are affected by perturbations due to both natural and anthropogenic factors. However, the assembly of bacterioplankton communities, either free-living (FL) or particle-associated, in coastal ecosystems is still poorly understood. Location: Coastal South China Sea influenced by the Pearl River (SCSPR). Methods: In this study, we investigated FL, nanoparticle-associated (NA) and microparticle-associated (MA) bacterial communities in the SCSPR, using environmental DNA metabarcoding based on the V4 region of the 16S rRNA gene. We assessed the relative importance of ecological processes using null model analyses based on a two-step framework. Results: We found that the observed amplicon sequence variants (ASVs) increased from FL, NA to MA communities, and a remarkably pervasive core set of ASVs closely belonged to potential hydrocarbonoclastic bacteria with wide habitat niche breadths. Analyses of similarity tests revealed that FL, NA and MA communities differed significantly but weakly, based on unweighted (R = 0.27, p <.001) and weighted (R = 0.18, p <.001) dissimilarities. Fundamental regulation of bacterial communities via homogeneous selection was most prominent in FL (90%), followed by NA (86.8%) and MA (73.3%), whereas the relative importance of dispersal limitation was most pronounced in MA (13.2%), followed by NA (11.7%) and FL (8.6%). Main conclusions: Bacterial communities in the SCSPR can be predominantly influenced by human activities, as indicated by the core ASVs closely related to hydrocarbonoclastic bacteria. Importantly, anthropogenic influences can temporally overwhelm the large environmental heterogeneities in coastal ecosystems. This study fills knowledge gaps in bacterial community ass

Mesoscale eddies are ubiquitous oceanographic features that influence the metabolism and community structure of Synechococcus. However, the metabolic adaptations of this genus to eddy-associated environmental changes have rarely been studied. We recovered two high-quality Synechococcus metagenome-assembled genomes (MAGs) from eddies in the South China Sea and compared their metabolic variations using metatranscriptomic samples obtained at the same time. The two MAGs (syn-bin1 and syn-bin2) are affiliated with marine Synechococcus subclusters 5.2 (S5.2) and 5.3 (S5.3), respectively. The former exhibited a higher abundance at the surface layer, whereas the latter was more abundant in the deep euphotic layer. Further analysis indicated that syn-bin1 had a strong ability to utilize organic nutrients, which could help it to thrive in the nutrient-deprived surface water. By contrast, syn-bin2 had the genetic potential to perform chromatic acclimation, which could allow it to capture green or blue light at different depths. Additionally, transcriptomic analysis showed that syn-bin2 upregulated genes involved in the synthesis of C4 acids, photosystem II proteins, and (Formula presented.) transporters in the deep euphotic layer, which might contribute to its predominance in low-light environments. Overall, this study expands our understanding of oceanic S5.2 and S5.3 Synechococcus by revealing their metabolic adaptations to mesoscale eddies. © 2021 The Authors. New Phytologist © 2021 New Phytologist Foundation