Patterns in Benthic Microbial Community Structure Across Environmental Gradients in the Beaufort Sea Shelf and Slope

Microbial profiling of the East Siberian Sea sediments using 16S rRNA gene and metagenome sequencing

The Arctic Ocean is experiencing significant global warming, leading to reduced sea-ice cover, submarine permafrost thawing, and increased river discharge. The East Siberian Sea (ESS) undergoes more significant terrestrial inflow from coastal erosion and river runoff than other Arctic seas. Despite extensive research on environmental changes, microbial communities and their functions in the ESS, which are closely related to environmental conditions, remain largely unexplored. Here, we investigated microbial communities in ESS surface sediments spanning latitudes from 73°N to 77°N using 16S rRNA amplicon sequencing, and reconstructed 211 metagenome-assembled genomes (MAGs) using shotgun metagenome sequencing. Taxonomic analysis identified 209 bacterial MAGs, with the predominant phyla Pseudomonadota (n = 82), Actinobacteriota (n = 38), Desulfobacterota (n = 23), along with 2 archaeal MAGs of Thermoproteota. Notably, 86% of the MAGs (n = 183) could not be classified into known species, indicating the potential presence of novel and unidentified microorganisms in the ESS. This dataset provides invaluable information on the microbial diversity and ecological functions in the rapidly changing ESS.

Sub-Liquid and Atmospheric Measurement Instrument To Autonomously Monitor the Biochemistry of Natural Aquatic Ecosystems

Monitoring the biochemistry of aquatic ecosystems is critical to understanding the biogeochemical cycling induced by microorganisms. They play a vital role in climate-gaseous drivers associated with natural ecosystems, such as methane emission in wetlands and peatlands; gas cycling and fixation: methane, sulfur, carbon, and nitrogen; water quality assessment and remediation; monitoring oxygen saturation due to contamination and algal proliferation; and many more. Microorganisms interact with these environments inducing diurnal and seasonal changes that have been, to date, poorly characterized. To aid with the long-term in-situ monitoring of natural aquatic ecosystems, we designed a Sub-liquid and Atmospheric Measurement (SAM) instrument. This floating platform can autonomously measure various sub-liquid and atmospheric parameters over a long time. This paper describes the design of SAM and illustrates how its long-term operation can produce critical information to complement other standard laboratory-based microbiological studies.

Unravelling microalgal-bacterial interactions in aquatic ecosystems through 16S rRNA gene-based co-occurrence networks

Interactions between microalgae and bacteria can directly influence the global biogeochemical cycles but the majority of such interactions remain unknown. 16S rRNA gene-based co-occurrence networks have potential to help identify microalgal-bacterial interactions. Here, we used data from 10 Earth microbiome projects to identify potential microalgal-bacterial associations in aquatic ecosystems. A high degree of clustering was observed in microalgal-bacterial modules, indicating densely connected neighbourhoods. Proteobacteria and Bacteroidetes predominantly co-occurred with microalgae and represented hubs of most modules. Our results also indicated that species-specificity may be a global characteristic of microalgal associated microbiomes. Several previously known associations were recovered from our network modules, validating that biologically meaningful results can be inferred using this approach. A range of previously unknown associations were recognised such as co-occurrences of Bacillariophyta with uncultured Planctomycetes OM190 and Deltaproteobacteria order NB1-j. Planctomycetes and Verrucomicrobia were identified as key associates of microalgae due to their frequent co-occurrences with several microalgal taxa. Despite no clear taxonomic pattern, bacterial associates appeared functionally similar across different environments. To summarise, we demonstrated the potential of 16S rRNA gene-based co-occurrence networks as a hypothesis-generating framework to guide more focused research on microalgal-bacterial associations.

Teasing apart the host-related, nutrient-related and temperature-related effects shaping the phenology and microbiome of the tropical seagrass Halophila stipulacea

BACKGROUND

Halophila stipulacea seagrass meadows are an ecologically important and threatened component of the ecosystem in the Gulf of Aqaba. Recent studies have demonstrated correlated geographic patterns for leaf epiphytic community composition and leaf morphology, also coinciding with different levels of water turbidity and nutrient concentrations. Based on these observations, workers have suggested an environmental microbial fingerprint, which may reflect various environmental stress factors seagrasses have experienced, and may add a holobiont level of plasticity to seagrasses, assisting their acclimation to changing environments and through range expansion. However, it is difficult to tease apart environmental effects from host-diversity dependent effects, which have covaried in field studies, although this is required in order to establish that differences in microbial community compositions among sites are driven by environmental conditions rather than by features governed by the host.

RESULTS

In this study we carried out a mesocosm experiment, in which we studied the effects of warming and nutrient stress on the composition of epiphytic bacterial communities and on some phenological traits. We studied H. stipulacea collected from two different meadows in the Gulf of Aqaba, representing differences in the host and the environment alike. We found that the source site from which seagrasses were collected was the major factor governing seagrass phenology, although heat increased shoot mortality and nutrient loading delayed new shoot emergence. Bacterial diversity, however, mostly depended on the environmental conditions. The most prominent pattern was the increase in Rhodobacteraceae under nutrient stress without heat stress, along with an increase in Microtrichaceae. Together, the two taxa have the potential to maintain nitrate reduction followed by an anammox process, which can together buffer the increase in nutrient concentrations across the leaf surface.

CONCLUSIONS

Our results thus corroborate the existence of environmental microbial fingerprints, which are independent from the host diversity, and support the notion of a holobiont level plasticity, both important to understand and monitor H. stipulacea ecology under the changing climate.

The relationship between dietary trophic level, parasites and the microbiome of Pacific walrus (Odobenus rosmarus divergens)

Arctic species are likely to experience rapid shifts in prey availability under climate change, which may alter their exposure to microbes and parasites. Here, we describe fecal bacterial and macroparasite communities and assess correlations with diet trophic level in Pacific walruses harvested during subsistence hunts by members of the Native Villages of Gambell and Savoonga on St Lawrence Island, Alaska. Fecal bacterial communities were dominated by relatively few taxa, mostly belonging to phyla Fusobacteriota and Firmicutes. Members of parasite-associated phyla Nematoda, Acanthocephala and Platyhelminthes were prevalent in our study population. We hypothesized that high versus low prey trophic level (e.g. fish versus bivalves) would result in different gut bacterial and macroparasite communities. We found that bacterial community structure correlated to diet, with nine clades enriched in walruses consuming higher-trophic-level prey. While no parasite compositional differences were found at the phylum level, the cestode genus Diphyllobothrium was more prevalent and abundant in walruses consuming higher-trophic-level prey, probably because fish are the intermediate hosts for this genus. This study suggests that diet is important for structuring both parasite and microbial communities of this culturally and ecologically important species, with potential implications for population health under climate change.

Insights into the bacterial community composition of farmed Caulerpa lentillifera: A comparison between contrasting health states

The bacterial communities of Caulerpa lentillifera were studied during an outbreak of an unknown disease in a sea grape farm from Vietnam. Clear differences between healthy and diseased cases were observed at the order, genus, and Operational Taxonomic Unit (OTU) level. A richer diversity was detected in the diseased thalli of C. lentillifera, as well as the dominance of the orders Flavobacteriales (phylum Bacteroidetes) and Phycisphaerales (Planctomycetes). Aquibacter, Winogradskyella, and other OTUs of the family Flavobacteriaceae were hypothesized as detrimental bacteria, this family comprises some well-known seaweed pathogens. Phycisphaera together with other Planctomycetes and Woeseia were probably saprophytes of C. lentillifera. The Rhodobacteraceae and Rhodovulum dominated the bacterial community composition of healthy C. lentillifera. The likely beneficial role of Bradyrhizobium, Paracoccus, and Brevundimonas strains on nutrient cycling and phytohormone production was discussed. The bleaching of diseased C. lentillifera might not only be associated with pathogens but also with an oxidative response. This study offers pioneering insights on the co-occurrence of C. lentillifera-attached bacteria, potential detrimental or beneficial microbes, and a baseline for understanding the C. lentillifera holobiont. Further applied and basic research is urgently needed on C. lentillifera microbiome, shotgun metagenomic, metatranscriptomic, and metabolomic studies as well as bioactivity assays are recommended.