Biology subjects

West-Roberts, J. A.

Publications and source records attributed to West-Roberts, J. A..

4 recordsLinked to original sources

bioRxiv2023

Infant gut bacteriophage strain persistence during the first three years of life

Bacteriophages are key components of gut microbiomes, yet the phage colonization process in the infant gut remains uncertain. Here, we established a large phage sequence database and used strain-resolved analyses to investigate phage succession in infants throughout the first three years of life. Analysis of 819 fecal metagenomes collected from 28 full-term and 24 preterm infants and their mothers revealed that early-life phageome richness increased over time and reached adult-like complexity by age three. Approximately 9% of early phage colonizers, mostly maternally transmitted and infecting Bacteroides, persisted for three years and were more prevalent in full-term than in preterm infants. Although rare, phages with stop codon reassignment were more likely to persist than non-recoded phages and generally displayed an increase in in-frame re-assigned stop codons over three years. Overall, maternal seeding, stop codon reassignment, host CRISPR-Cas locus prevalence, and diverse phage populations contribute to stable viral colonization.

microbiology↗

bioRxiv2022

Do lanthanide-dependent microbial metabolisms drive the release of REEs from weathered granites?

Prior to soil formation, phosphate liberated by rock weathering is often sequestered into highly insoluble lanthanide phosphate minerals. Dissolution of these minerals is critical for the release of phosphate to the biosphere, yet the microorganisms involved, and the genes required for lanthanide metabolism, are poorly understood. Here, we sampled weathered granite and associated soil to identify the zones of lanthanide phosphate mineral solubilization and genomically define the organisms implicated in lanthanide utilisation. We reconstructed 136 genomes from 11 bacterial phyla and found gene clusters implicated in lanthanide-based metabolism of methanol (primarily XoxF3 and XoxF5) are surprisingly common in microbial communities in moderately weathered granite where lanthanide phosphate minerals are dissolving. Notably, XoxF3 systems were found in Verrucomicrobia for the first time, and in Acidobacteria, Gemmatimonadetes, and Alphaproteobacteria. The XoxF-containing gene clusters are shared by diverse Acidobacteria and Gemmatimonadetes, and include conserved hypothetical proteins and transporters not associated with the few well studied XoxF systems. Given that siderophore-like molecules that strongly bind lanthanides may be required to solubilize lanthanide phosphates, it is notable that candidate siderophore biosynthesis systems were most prevalent in bacteria in moderately weathered rock, especially in Acidobacteria with lanthanide-based systems. We conclude that the confluence in the zone of moderate weathering of phosphate mineral dissolution, lanthanide utilisation, and methanol oxidation (thus carbonic acid production) may be important during the conversion of granitic rock to soil.

microbiology↗

bioRxiv2022

A widespread group of large plasmids in methanotrophic Methanoperedens archaea

Anaerobic methanotrophic (ANME) archaea conserve energy from the breakdown of methane, an important driver of global warming, yet the extrachromosomal genetic elements that impact the activities of ANME archaea are little understood. Here we describe large plasmids associated with ANME archaea of the Methanoperedens genus. These have been maintained in two bioreactors that contain enrichment cultures dominated by different Methanoperedens species and co-occur with Methanoperedens species in other anoxic environments. By manual curation we show that two of the plasmids are large (155,607 bp and 191,912 bp), circular, and replicate bidirectionally. The group of Methanoperedens species that carry these plasmids is related to "Ca. Methanoperedens nitroreducens", "Ca. Methanoperedens ferrireducens", "Ca. Methanoperedens manganicus" and the plasmids occur in the same copy number as the main chromosome. The larger plasmid encodes transporters that potentially enhance access to Ni, which is required for the methyl-CoM reductase (Mcr), Co required for the cobalamin cofactor needed for methyltransferases, and amino acid uptake. We show that many plasmid genes are actively transcribed, including genes involved in plasmid chromosome maintenance and segregation, a Co2+/Ni2+ transporter and cell protective proteins. Notably, one plasmid carries three tRNAs and two colocalized genes encoding ribosomal protein uL16 and elongation factor eEF2. These are not encoded in the host Methanoperedens genome and uL16 and eEF2 were highly expressed, indicating an obligate interdependence between this plasmid and its host. The finding of plasmids of Methanoperedens opens the way for the development of genetic vectors that could be used to probe little understood aspects of Methanoperedens physiology. Ultimately, this may provide a route to introduce or alter genes that may enhance growth and overall metabolism to accelerate methane oxidation rates.

microbiology↗

bioRxiv2021

The Chloroflexi supergroup is metabolically diverse and representatives have novel genes for non-photosynthesis based CO2 fixation

The Chloroflexi superphylum have been investigated primarily from the perspective of reductive dehalogenation of toxic compounds, anaerobic photosynthesis and wastewater treatment, but remain relatively little studied compared to their close relatives within the larger Terrabacteria group, including Cyanobacteria, Actinobacteria, and Firmicutes. Here, we conducted a detailed phylogenetic analysis of the phylum Chloroflexota, the phylogenetically proximal candidate phylum Dormibacteraeota, and a newly defined sibling phylum proposed in the current study, Eulabeiota. These groups routinely root together in phylogenomic analyses, and constitute the Chloroflexi supergroup. Chemoautotrophy is widespread in Chloroflexi. Two Form I Rubisco ancestral subtypes that both lack the small subunit are prevalent in ca. Eulabeiota and Chloroflexota, suggesting that the predominant modern pathway for CO2 fixation evolved in these groups. The single subunit Form I Rubiscos are inferred to have evolved prior to oxygenation of the Earths atmosphere and now predominantly occur in anaerobes. Prevalent in both Chloroflexota and ca. Eulabeiota are capacities related to aerobic oxidation of gases, especially CO and H2. In fact, aerobic and anaerobic CO dehydrogenases are widespread throughout every class-level lineage, whereas traits such as denitrification and reductive dehalogenation are heterogeneously distributed across the supergroup. Interestingly, some Chloroflexota have a novel clade of group 3 NiFe hydrogenases that is phylogenetically distinct from previously reported groups. Overall, the analyses underline the very high level of metabolic diversity in the Chloroflexi supergroup, suggesting the ancestral metabolic platform for this group enabled highly varied adaptation to ecosystems that appeared in the aerobic world.

microbiology↗