Biology subjects

Mara, P.

Publications and source records attributed to Mara, P..

3 recordsLinked to original sources

bioRxiv2023

PCR-based survey of methane-cycling archaea in methane-soaked subsurface sediments of Guaymas Basin, Gulf of California

The Guaymas Basin in the Gulf of California is characterized by active seafloor spreading, rapid deposition of organic-rich sediments, steep geothermal gradients, and abundant methane of mixed thermogenic and microbial origin. Subsurface sediment samples from eight drilling sites with distinct geochemical and thermal profiles were selected for DNA extraction and PCR amplicifation to explore the diversity of methane-cycling archaea in the Guaymas Basin subsurface. We performed PCR amplifications with general (mcrIRD), and ANME-1 specific primers that target the alpha () subunit of methyl coenzyme M reductase (mcrA). Diverse ANME-1 lineages associated with anaerobic methane oxidation were detected in seven out of the eight drilling sites, preferentially around the methane-sulfate interface, and in several cases showed preferences for specific sampling sites. Phylogenetically, most ANME-1 sequences from the Guaymas Basin subsurface were related to marine mud volcanoes, seep sites, and the shallow marine subsurface. The most frequently recovered methanogenic phylotypes were closely affiliated with the hyperthermophilic Methanocaldococcaceae, and found at the hydrothermally influenced Ringvent site. The coolest drilling site, in the northern axial trough of Guaymas Basin, yielded the greatest diversity of methanogen lineages. Our survey indicates potential for extensive microbial methane cycling within subsurface sediments of Guaymas Basin.

microbiology↗

bioRxiv2023

Metagenomic Profiles of Archaea and Bacteria within Thermal and Geochemical Gradients of the Guaymas Basin Deep Subsurface

While the temperature gradients of Earths crust and sediments are thought to delineate the downward extent and ultimate limits of the subsurface biosphere, the actual course of consecutively changing microbial communities and activities, from cool surficial sediments towards the deep, hot biosphere, remains to be charted. We used metagenomic and metatranscriptomic analyses of the hydrothermally heated, massive sediment layers of Guaymas Basin (Gulf of California, Mexico) to examine the environmental distribution and activity patterns of bacteria and archaea along thermal, geochemical and cell count gradients. Composition and distribution of MAGs, dominated by Chloroflexota and Thermoproteota, were shaped by biogeochemical parameters as long as temperatures remained moderate, but downcore increasing temperatures overrode other factors beyond ca. 45{degrees}C. Consistently, MAG genome size and diversity decreased with increasing temperature, indicating a conspicuous downcore winnowing of the subsurface biosphere. In contrast, specific archaeal MAGs within the Thermoproteota and Hadarchaeota increased in relative abundance and in recruitment of transcriptome reads towards deeper, hotter sediments, and mark the transition towards a distinct deep, hot biosphere.

bioinformatics↗

bioRxiv2022

Diverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently anoxic Cariaco Basin

Secondary metabolites play essential roles in ecological interactions and nutrient acquisition, and are of interest for their potential uses in medicine and biotechnology. Under laboratory conditions the discovery of new compounds is hindered by low production, high rediscovery rates, and detection evasion. Genome mining for biosynthetic gene clusters (BGCs) is a popular approach to address these limitations, thereby uncovering often cryptic secondary metabolic potential. Marine systems are often underrepresented in bulk genome mining efforts; and habitats with unique physicochemical characteristics such as oxygen-depleted and anoxic water columns remain virtually unexplored regarding BGCs. Here, we use genome mining and differential gene expression analyses to show that redox potential and particle-associated vs. free-living lifestyles both influence the composition and production of secondary metabolites through the stratified water column of the Cariaco Basin, Venezuela. Microbiota, including understudied clades, such as Planctomycetota, encode and express a wide range of secondary metabolites in these anoxic/euxinic waters.

bioinformatics↗