Biology subjects

Bik, H.

Publications and source records attributed to Bik, H..

3 recordsLinked to original sources

bioRxiv2026

MeioBIOME: A snakemake workflow for the parallel analysis of meiofaunal genomes and host-associated bacteria/archaea

Microbes closely interact with every living organism, including meiofauna (i.e., microbial eukaryotes 38 m - 1 mm in length), and influence the development, life cycle, and evolution of diverse metazoans. Together, meiofauna and their microbiomes, collectively referred to as the holobiont, underpin biogeochemical cycles and drive decomposition of organic matter. However, our understanding of the ecological and evolutionary dynamics of meiofauna microbiomes are limited, typically owed to low-resolution 16S rRNA surveys, which cannot accurately delineate bacterial taxa. Single-specimen holobiont sequencing can help overcome the limitations of metabarcoding approaches by 1) generating metagenome-assembled genomes (MAGs) of the host microbiome and 2) recovering host single-copy genes (SCGs) to phylogenetically confirm the identity of the host organism. However, most bioinformatics pipelines for the assembly of metagenomic datasets have been developed for the assembly of high-complexity microbial communities of bulk sediment or soil samples (and cannot be used for the assembly of host genomes), rely on co-assembly approaches (which collapses strain-level genomic information of bacterial taxa), and focus on binning either prokaryotic or eukaryotic taxa. Therefore, there is a tremendous need for a computational workflow for the dual analysis of host genomes and their microbiomes. Here, we developed MeioBIOME, a modular Snakemake pipeline for the reproducible analysis of holobiont metagenomes obtained from individually sequenced microbial metazoa. We analyze publicly available single-specimen metagenomics datasets to show the utility of MeioBIOME and recover host-associated symbiont MAGs and host SCGs. Additionally, we integrate state-of-the-art binning algorithms which generate more MAGs than the DOE Joint Genome Institute metagenomic pipeline. We anticipate that MeioBIOME will facilitate studies of phylosymbiosis by generating high-quality host genome skims (to build well-supported host phylogenetic trees) and host-associated prokaryotic MAGs obtained from single specimens.

bioinformatics↗

bioRxiv2026

Environmental gradients and habitat specificity structure benthic microbial assemblages in a temperate seagrass ecosystem

Seagrass meadows are globally distributed coastal ecosystems that provide habitats for diverse species and facilitate ecosystem services, such as carbon storage and nutrient cycling. However, factors linked to human activities and climate change are causing seagrass decline worldwide, thus impacting benthic community structure and ecosystem functioning. Although macrofaunal communities in seagrass habitats are well studied, the structure and function of bacteria/archaea and microeukaryote assemblages remains underexplored. In this study, we used environmental DNA (eDNA) metabarcoding (16S and 18S rRNA genes) to analyze bacteria/archaea (16S), microeukaryotes (18S raw sediment), and meiofauna (18S Ludox) communities in seagrass and bare sediment habitats across three sites along an estuarine gradient in Bodega Harbor, California. We found that microbial and microeukaryote communities were primarily structured by site as a response to the environmental gradient (e.g., sediment properties), whereas meiofauna responded more strongly to the presence of seagrass. Beta diversity showed strong differentiation among estuarine sites, while alpha diversity varied within sites, with bare sediments often displaying higher diversity. Network analysis revealed significant co-occurrences between bacteria and nematodes, including chemosynthetic symbiont-bearing lineages in mudflats and stress-tolerant bioindicators. Our findings underscore the importance of environmental gradients and microhabitat features in shaping benthic biodiversity in temperate seagrass ecosystems. Furthermore, it highlights potential microbial-nematode associations, likely a response to environmental variation. By integrating multiple benthic components, our study advances understanding of biodiversity drivers in temperate estuarine seagrass habitats and provides new insights on microbial community structure in these ecosystems. ImportanceSeagrass meadows, which sustain a wide variety of plant and animal life, are vital coastal habitats. These submerged ecosystems support biodiversity, protection of coasts, nitrogen cycling, and carbon storage. However, they are declining due to pressures from climate change and human activity. This study characterizes the microbial and microeukaryote communities, including meiofauna, that inhabit and surround temperate seagrass meadows. By analyzing these communities across different areas of Bodega Harbor, California, we demonstrate how seagrass and environmental factors affect the resilience and overall health of the ecosystem. Our findings highlight the importance of seagrass in maintaining biodiversity and suggest that microscale interactions and habitat variation are important factors shaping these temperate coastal ecosystems. A comprehensive understanding of the variation within benthic communities associated with seagrass habitats can significantly enhance conservation and restoration efforts for seagrass meadows..

ecology↗

bioRxiv2023

100 years of anthropogenic impact causes changes in freshwater functional biodiversity

Despite efforts from scientists and regulators, biodiversity is declining at an alarming rate. Unless we find transformative solutions to preserve biodiversity, future generations may not be able to enjoy natures services. We have developed a conceptual framework that establishes the links between biodiversity dynamics and abiotic change through time and space using artificial intelligence. Here, we apply this framework to a freshwater ecosystem with a known history of human impact and study 100 years of community-level biodiversity, climate change and chemical pollution trends. We apply explainable network models with multimodal learning to community-level functional biodiversity measured with multilocus metabarcoding, to establish correlations with biocides and climate change records. We observed that the freshwater community assemblage and functionality changed over time without returning to its original state, even if the lake partially recovered in recent times. Insecticides and fungicides, combined with extreme temperature events and precipitation, explained up to 90% of the functional biodiversity changes. The community-level biodiversity approach used here reliably explained freshwater ecosystem shifts. These shifts were not observed when using traditional quality indices (e.g. Trophic Diatom Index). Our study advocates the use of high throughput systemic approaches on long-term trends over species-focused ecological surveys to identify the environmental factors that cause loss of biodiversity and disrupt ecosystem functions.

ecology↗