Biology subjects

Wipfler, R. L.

Publications and source records attributed to Wipfler, R. L..

4 recordsLinked to original sources

bioRxiv2025

Diversity and single-cell activity of endolithic microbes in sediment-hosted carbonate nodules within and below the sulfate-methane transition zone

Authigenic carbonate concretions ( nodules) precipitate in marine seep sediments as a result of anaerobic oxidation of methane (AOM). These rocks host active endolithic microbial communities and persist as important methane sinks. Still, how these communities and their activity differ from those in adjacent seep sediments, particularly as a function of proximity to the sulfate-methane transition zone (SMTZ), remains understudied. Here, we sampled sediments and nodules within and below the SMTZ (0-57 cm deep) at four active deep-sea seep areas in Santa Monica Basin, CA. Measurements of high nodule porosities (43-51%) coupled to strong similarities between sediment and nodule 16S rRNA-based community profiles, including below the SMTZ, suggest continued perfusion and exchange between buried nodules and surrounding sediment. Shared, depth-dependent transitions in methanotrophic taxa (ANME-1, ANME-2, ANME-3) and methanogenic taxa (Methanofastidiosales) below the SMTZ were also consistent with trends in porewater methane and sulfate concentrations, porewater DIC, and nodule {delta}13C values -- underscoring the impact of different geochemical conditions on community structure and suggestive of under-characterized physiological plasticity in ANME-1. Laboratory-based BONCAT incubations of nodules within the SMTZ over [~]14-weeks revealed active sulfide production and translationally active endolithic microorganisms. However, cells from parallel nodule incubations recovered below the SMTZ showed weak-to-negligible BONCAT-based activity despite similar cell abundances -- suggestive of low activity on shorter timescales or dormancy. Together, these data challenge the interpretation of passively recorded microbiological signatures in seep sediment-hosted carbonate nodules and expand our understanding of how these endolithic communities may be actively shaped by past and present conditions. ImportanceThis study advances earlier investigations of microbial communities in buried seep carbonate nodules by integrating microbiological profiles of nodules and sediments, sediment geochemistry, single-cell activity measurements, and nodule mineral, geochemical, and physical characteristics within and below the sulfate-methane transition zone in deep-sea methane seeps. This approach allows us to view how nodule-hosted, endolithic microbial communities change relative to their surrounding sediments across multiple geochemical contexts and better understand how formation history and environmental conditions might affect community identity and metabolic function. Results indicate that the seep nodule and surrounding sediment communities are closely linked across diverse geochemical conditions. This connectivity between sediments and carbonate nodules is distinct from that observed in exhumed seep carbonates, with implications regarding how microbial community composition within these nodules are interpreted, suggesting that instead of a passive recorder of the communities at the time of formation, these nodules appear to retain diverse, metabolically viable communities.

microbiology↗

bioRxiv2024

Spatial evidence of cryptic methane cycling and methylotrophic metabolisms along a land-ocean transect in a California coastal wetland

Methylotrophic methanogenesis in the sulfate reduction zone of coastal and marine sediments couples with anaerobic methane oxidation (AOM), forming the cryptic methane cycle. This study provides evidence of cryptic methane cycling in the sulfate-reducing zone across a land-ocean transect of four stations--two brackish, one marine, and one hypersaline--within the Carpinteria Salt Marsh Reserve (CSMR), Southern California, USA. The top 20 cm of sediment from the transect underwent geochemical and molecular (16S rRNA) analyses, in-vitro methanogenesis incubations, and radiotracer incubations using 35S-SO4, 14C-mono-methylamine, and 14C-CH4. Sediment methane concentrations were consistently low (3 to 28 {micro}M) except at the marine station, where they increased with depth (max 665 {micro}M). Methanogenesis from mono-methylamine was detected throughout the sediment at all stations with estimated rates ranging between 0.14 and 3.8 nmol cm-3 d-1. 16S rRNA analysis identified methanogenic archaea capable of producing methane from methylamines in sediment where methanogenesis was found to be active. Metabolomic analysis of porewater showed mono-methylamine was mostly undetectable (<3 {micro}M) or present in trace amounts (<10 {micro}M) suggesting rapid metabolic turnover. In-vitro methanogenesis incubations showed no linear methane buildup, suggesting a process limiting methane emissions. AOM activity, measured with 14C-CH4, overlapped with methanogenesis from mono-methylamine activity at all stations, with rates ranging from 0.03 to 19.4 nmol cm-3 d-1. Porewater geochemical analysis showed the CSMR sediments are rich in sulfate and iron. Porewater sulfate concentrations (9-91 mM) were non-limiting across the transect, which support members of sulfate-reducing bacteria and likely responsible for sulfate reduction activity (1.5-2,506 nmol cm-3 d-1) at all stations in the CSMR. Porewater sulfide and iron (II) profiles indicated that the sediment transitioned from a predominantly iron-reducing environment at the two brackish stations to a predominantly sulfate-reducing environment at the marine and hypersaline station. AOM activity was likely coupled to sulfate and possibly iron reduction, coinciding with the presence of anaerobic methanotrophs and bacteria involved in these reductions. 16S rRNA analysis identified anaerobic methanotrophs at the marine and hypersaline stations, where they coexisted with putative methanogens, suggesting both groups, or methanogens alone, may be involved in cryptic methane cycling, preventing significant methane buildup in the sulfate-reducing zone. Differences in rate constants from 14C radiotracer incubations suggest a non-methanogenic process oxidizing mono-methylamine to inorganic carbon, likely mediated by sulfate-reducing bacteria. Understanding the potential competition of sulfate reducers with methanogens for mono-methylamine needs further investigation as it might be another important process responsible for low methane emissions in salt marshes.

microbiology↗

bioRxiv2018

Revealing S-layer Functions in the Hyperthermophilic Crenarchaeon Sulfolobus islandicus

The crystalline surface layer (S-layer), consisting of two glycoproteins SlaA and SlaB, is considered to be the exclusive component of the cell envelope outside of the cytoplasmic membrane in Sulfolobus species. Although biochemically and structurally characterized, the S-layer in vivo functions remain largely elusive in Archaea. Here, we investigate how the S-layer genes contribute to the S-layer architecture and affect cellular physiology in a crenarchaeal model, Sulfolobus islandicus M.16.4. Electron micrographs of mutant cells lacking slaA or both slaA and slaB confirm the absence of the outermost layer (SlaA), whereas cells with intact, partially, or completely detached SlaA are observed for the {triangleup}slaB mutant. Importantly, we identify a novel S-layer-associated protein M164_1049, which does not functionally replace its homolog SlaB but likely assists SlaB to stabilize SlaA. Additionally, we find that mutants deficient in SlaA form large cell aggregates and the individual cell size varies significantly. The slaB gene deletion also causes noticeable cellular aggregation, but the size of those aggregates is smaller when compared to {triangleup}slaA and {triangleup}slaAB mutants. We further show the {triangleup}slaA mutant cells exhibit more sensitivity to hyperosmotic stress but are not reduced to wild-type cell size. Finally, we demonstrate that the {triangleup}slaA mutant contains aberrant chromosome copy numbers not seen in wild-type cells where the cell cycle is tightly regulated. Together these data suggest that the lack of slaA results in either cell fusion or irregularities in cell division. Our studies provide novel insights into the physiological and cellular functions of the S-layer in Archaea.\n\nSignificanceRediscovery of the ancient evolutionary relationship between archaea and eukaryotes has revitalized interest in archaeal cell biology. Key to understanding the archaeal cell is the S-layer which is ubiquitous in Archaea but whose in vivo function is unknown. In this study, we genetically dissect how the two well-known S-layer genes as well as a newly identified S-layer-associated-protein-encoding gene contribute to the S-layer architecture in a hyperthermophilic crenarchaeal model S. islandicus. We provide genetic evidence for the first time showing that the slaA gene is a key cell morphology determinant and may play a role in Sulfolobus cell division or cell fusion.

microbiology↗

bioRxiv2018

The essential genome of the crenarchaeal model Sulfolobus islandicus

Sulfolobus islandicus is a model experimental system in the TACK superphylum of the Archaea, a key lineage in the evolutionary history of cell biology. Here we report a genome-wide identification of the repertoire of genes essential to S. islandicus growth in culture. We confirm previous targeted gene knockouts, uncover the non-essentiality of functions assumed to be essential to the Sulfolobus cell, including the proteinaceous S-layer, and highlight key essential genes whose functions are yet to be determined. Phyletic distributions illustrate the potential transitions that have occurred during the evolution of this contemporary archaeal cell and highlight the sets of genes that may have been associated with each transition. We use this comparative context as a lens to focus future research on archaea-specific uncharacterized essential genes for which future functional data would provide valuable insights into the evolutionary history of the contemporary cell.

microbiology↗