Biology subjects

Woodhouse, J. N.

Publications and source records attributed to Woodhouse, J. N..

3 recordsLinked to original sources

bioRxiv2024

Suspended and sinking particle-associated microbiomesexhibit distinct lifestyles in the Elbe estuary

Estuaries are important components of the global carbon cycle; exchanging carbon between aquatic, atmospheric, and terrestrial environments, representing important loci for blue carbon storage and greenhouse gas emissions. Estuarine particles are especially important due to their microbial transformation and vertical/horizontal transport. We used metagenomes and metatranscriptomes to assess changes in microbial community composition and functions across the Elbe estuary over one year, linking changes to dissolved and particulate organic matter. We will be the first to link microbial activity derived from molecular data to particulate and dissolved organic carbon characteristics. There were no microbial species responses to the measured physicochemical and dissolved/particulate organic matter parameters, however Weighted Correlation Network Analyses showed significant spatial microbiome differences linked to the estuarine salinity profile. Meanwhile, suspended and sinking particle fractions did not show any community wide differences, but individual gene analyses revealed clear microbial lifestyle differences. Sinking particle-associated transcripts highly expressed competition and stress-responses genes, while suspended particle-associated transcripts favoured energy acquisition and growth. Transcription patterns further indicate that suspended particles may represent a mitigating influence on methane release via methanotrophy, while both suspended and sinking particles produce methane through the same gene complex. This notion suggests that increased sinking particle abundance, such as under high turbidity conditions, leads to increased methane production. Our findings further imply that urban activities such as dredging may have a high impact on greenhouse gas emissions, and higher suspended-sinking particle ratios may alleviate aquatic-atmospheric methane exchanges. Future studies should explore in detail the underlying mechanisms and controlling variables, in particular when taking predicted global changes into account.

ecology↗

bioRxiv2024

Environmental controls of dark CO2 fixation in wetland microbiomes

Rising atmospheric concentration of CO2 is a major concern to society due to its global warming potential. In soils, CO2 fixing microorganisms are preventing a part of the CO2 from entering the atmosphere. Yet, the pathways behind dark CO2 fixation are rarely studied in situ. Here we examined the environmental controls on the abundance and expression of key genes involved in microbial CO2 fixation in estuarine wetlands. A combined multi-omics approach incorporating metabarcoding, deep metagenomic and metatranscriptomic analyses confirmed that wetland microbiota harbor all six known CO2 fixation pathways and that these pathways are transcribed at high frequencies along several environmental gradients, albeit at different levels depending on the environmental niche. Notably, the transcription of the key genes for the reductive tricarboxylic acid cycle (rTCA) and the Calvin cycle were favored by low salinity and O2 rich niches high in organic matter, while the transcription of the key genes for the Wood-Ljungdahl pathway (WLP) and dicarboxylate/4-hydroxybutyrate cycle (DC/4-HB cycle) were favored by low O2 niches poor in organic matter. Taxonomic assignment of transcripts implied that dark CO2 fixation was mainly linked to few bacterial phyla, namely, Desulfobacterota, Gemmatimonadota, Methylomirabilota, Nitrospirota and Pseudomonadota.

microbiology↗

bioRxiv2019

Taxonomical and functional diversity of Saprolegniales in Anzali lagoon, Iran

Studies on the diversity, distribution and ecological role of Saprolegniales (Oomycota) in freshwater ecosystems are currently receiving attention due to a greater understanding of their role in carbon cycling in various aquatic ecosystems. In this study, we characterized several Saprolegniales species isolated from Anzali lagoon, Gilan province, Iran, using morphological and molecular methods. Four species of Saprolegnia were identified, including S. anisospora and S. diclina as first reports for Iran. Evaluation of the ligno-, cellulo- and chitinolytic activities were also measured using plate assay methods. Most of the Saprolegniales isolates were obtained in autumn and nearly 50% of the strains showed chitinolytic and cellulolytic activities. However, only a few Saprolegniales strains showed lignolytic activities. This study has important implications for better understanding the ecological niche of oomycetes, and to differentiate them from morphologically similar but functional different aquatic fungi in freshwater ecosystems.

ecology↗