Biology subjects

Biddle, J.

Publications and source records attributed to Biddle, J..

5 recordsLinked to original sources

bioRxiv2021

Helarchaeota and Co-occurring Sulfate-Reducing Bacteria in Subseafloor Sediments from the Costa Rica Margin

Deep sediments host many archaeal lineages, including those of the Asgard superphylum that may depend on/require syntrophic partnerships. Our knowledge about sedimentary archaeal diversity and their metabolic pathways and syntrophic partners is still very limited. We present here new genomes of Helarchaeota and co-occurring sulfate-reducing bacteria (SRB) recovered from organic-rich sediments off Costa Rica Margin. Our molecular analyses revealed three new metagenome-assembled genomes (MAGs) affiliating with Helarchaeota, each of which has three variants of the methyl-CoM reductase-like (MCR-like) complex that may enable them to oxidize short-chain alkanes anaerobically. These Helarchaeota have no multi-heme cytochromes (MHCs) but have Group 3b and Group 3c [NiFe] hydrogenases, and formate dehydrogenase, and therefore could transfer the reducing equivalents generated from alkane oxidation to external partners via the transfer of these substances. We also recovered five MAGs of SRB affiliated with the class of Desulfobacteria, two of which showed relative abundances (represented by genome coverages) positively correlated with those of the three Helarchaeota. Genome analysis suggested that these SRB bacteria have the capacity of H2 and formate utilizations and may facilitate electron transfers from other organisms by means of these reduced substances. Our findings suggest that Helarchaeota may metabolize synergistically with SRB in marine anoxic sediments, and exert an important influence on the carbon cycle by mitigating the hydrocarbon emission from sediments to the overlying ocean.

microbiology↗

bioRxiv2020

Sifarchaeota a novel Asgard phylum capable of polysaccharide degradation and anaerobic methylotrophy

The Asgard superphylum is a deeply branching monophyletic group of Archaea, recently described as some of the closest relatives of the eukaryotic ancestor. The wide application of genomic analyses from metagenome sequencing has established six distinct phyla, whose genomes encode for diverse metabolic capacities and play important biogeochemical and ecological roles in marine sediments. Here, we describe two metagenome-assembled genomes (MAGs) recovered from deep marine sediments off Costa Rica margin, defining a novel lineage phylogenetically married to Thorarchaeota, as such we propose the name "Sifarchaeota" for this phylum. The two "Sifarchaeota" MAGs encode for an anaerobic methylotrophy pathway enabling the utilization of C1-C3 compounds (methanol and methylamines) to synthesize acetyl CoA. Also, the MAGs showed a remarkable saccharolytic capabilities compared to other Asgard lineages and encoded for diverse classes of carbohydrate active enzymes (CAZymes) targeting different mono-, di- and oligosaccharides. Comparative genomic analysis based on the full metabolic profiles of Asgard lineages revealed the close relation between "Sifarchaeota" and Odinarchaeota MAGs, which suggested a similar metabolic potentials and ecological roles. Furthermore, we identified multiple potential horizontal gene transfer (HGT) events from different bacterial donors within "Sifarchaetoa" MAGs, which hypothetically expanded "Sifarchaeota" capacities for substrate utilization, energy production and niche adaptation. ImportanceDeep marine sediments are the home of multiple poorly described archaeal lineages, many of which have ecological and evolutionary importance. We recovered metagenome-assembled genomes (MAGs) belonging to a novel Asgard phylum from the deep sediment of the Costa Rica margin. We proposed the name "Sifarchaeota" to describe the members of this phylum. Representative genomes of the "Sifarchaeota" showed remarkable saccharolytic capacities extending the known metabolic features encoded by the Asgard lineages. We attribute its ability to survive under the deep sediment conditions to its putative capacities to utilize different (C1-C3) compounds commonly encountered in deep sediment environments via anaerobic methylotrophy pathway. Also, we showed the importance of horizontal gene transfer in enhancing the "Sifarchaeota" collective adaptation strategies.

microbiology↗

bioRxiv2020

Evidence for an expanded repertoire of electron acceptors for the anaerobic oxidation of methane in authigenic carbonates in the Atlantic and Pacific Ocean

Authigenic carbonates represent a significant microbial sink for methane, yet little is known about the microbiome responsible for the methane removal. We identify carbonate microbiomes distributed over 21 locations hosted by 7 different cold seeps in the Pacific and Atlantic Oceans by carrying out a gene-based survey using 16S rRNA- and mcrA gene sequencing coupled with metagenomic analyses. These sites were dominated by bacteria affiliated to the Firmicutes, Alpha- and Gammaproteobacteria. ANME-1 and -2 clades were abundant in the carbonates yet their typical syntrophic partners, sulfate reducing bacteria, were not significantly present. Our analysis indicated that methane oxidizers affiliated to the ANME-1 and -2 as well as to the Candidatus Methanoperedens clades, are capable of performing complete methane- and potentially short-chain alkane oxidations independently using oxidized sulfur and nitrogen compounds as terminal electron acceptors. Gammaproteobacteria are hypothetically capable of utilizing oxidized nitrogen compounds in potential syntrophy with methane oxidizing archaea. Carbonate structures represent a window for a more diverse utilization of electron acceptors for anaerobic methane oxidation along the Atlantic and Pacific Margin.

microbiology↗

bioRxiv2019

Genomic expansion of archaeal lineages resolved from deep Costa Rica sediments

Numerous archaeal lineages are known to inhabit marine subsurface sediments, although their distributions, metabolic capacities and interspecies interactions are still not well understood. Abundant and diverse archaea were recently reported in Costa Rica (CR) margin subseafloor sediments recovered during IODP Expedition 334. Here, we recover metagenome-assembled genomes (MAGs) of archaea from the CR-margin and compare them to their relatives from shallower settings. We describe 31 MAGs of 6 different archaeal lineages (Lokiarchaeota, Thorarchaeota, Heimdallarchaeota, Bathyarcheota, Thermoplasmatales and Hadesarchaea) and thoroughly analyze representative MAGs from the phyla Lokiarchaeota and Bathyarchaeota. Our analysis suggests the potential capabilities of Lokiarchaeota members to anaerobically degrade aliphatic and aromatic hydrocarbons. We show it is genetically possible and energetically feasible for Lokiarchaeota to degrade benzoate if they associate with organisms using nitrate, nitrite and sulfite as electron acceptors, which suggests a possibility of syntrophic relationships between Lokiarchaeota and nitrite and sulfite reducers. The novel Bathyarchaeota lineage possesses an incomplete methanogenesis pathway lacking the methyl co-enzyme M reductase complex and encodes a non-canonical acetogenic pathway potentially coupling methylotrophy to acetogenesis via the methyl branch of Wood-Ljundahl pathway. These novel metabolic characteristics suggest the potential of this Bathyarchaeota lineage to be a transition between methanogenic and acetogenic Bathyarchaeota lineages. This work substantially expands our knowledge about the metabolic function repertoire of marine benthic archaea.

microbiology↗

bioRxiv2019

Discrete Community Assemblages Within Hypersaline Paleolake Sediments of Pilot Valley, Utah

Hypersaline paleolake sediments are understudied ecosystems whose microbial ecology is largely unknown. Here we present mineralogical, geochemical, and small-subunit 16S rRNA gene sequence data on one such environment, the Pilot Valley Basin (PVB), a sub-basin of ancient Lake Bonneville located in northwest Utah. PVB exhibits a variety of aqueous minerals including phyllosilicates, carbonates, and sulfates, as well as microbially-induced sedimentary structures. As perchlorate occurs naturally (up to 6.5 ppb) in Pilot Valley sediments, and because recent evidence suggests that it is subject to biotic reduction, PVB has been proposed as a Mars analog site for astrobiological studies. 16S rRNA gene sequencing was used to investigate microbial diversity and community structure along horizontal and vertical transects within the upper basin sediments and beta diversity analyses indicate that the microbial communities in Pilot Valley are structured into three discrete groups. Operational taxonomic units (OTUs) belonging to the main archaeal phylum, Euryarchaeota, make up ~23% of the sequences, while OTUs belonging to three bacterial phyla, Proteobacteria, Bacteroides and Gemmatimonadetes, constitute ~60-70% of the sequences recovered at all sites. Diversity analyses indicate that the specific composition of each community correlates with sediment grain size, and with biogeochemical parameters such as nitrate and sulfate concentrations. Interestingly, OTUs belonging to the phylum Gemmatimonadetes are co-located with extreme halophilic archaeal and bacterial taxa, which suggests a potential new attribute, halophilicity, of this newly-recognized phylum. Altogether, results of this first comprehensive geomicrobial study of Pilot Valley reveal that basin sediments harbor a complex and diverse ecosystem.

microbiology↗