Grand Challenges in Extreme Microbiology

As the microbiological exploration of our home planet intensifies, we discover that an ever-growing range of extreme environments harbors novel types of microorganisms. Wherever we look, previously unknown bacteria, archaea, and protists appear into view. Scientific perceptions of the microbial world and its “extreme” fringes have changed with increasing pace and with unforeseen consequences – and lead directly toward the grand research challenges for the future

Primary stability of cementless threaded acetabular cups at first implantation and in the case of revision regarding micromotions as indicators

The primary stability of cementless total hip endoprosthesis is of vital importance for proximate, long-term osteointegration. The extent of micromotions between implant and acetabulum is an indicator of primary stability. Based on this hypothesis, different cementless hip joint endoprosthesis were studied with regard to their micromotions. The primary stability of nine different cementless threaded acetabular cups was studied in an experimental setup with blocks of rigid foam. The micromotions between implant and implant bearing were therefore evaluated under cyclic, sinusoidal exposure. The blocks of polymer foam were prepared according to the Paprosky defect classifications. The micromotions increased with the increasing degree of the defect with all acetabuli tested. Occasionally coefficients of over 200 mu m were measured. From a defect degree of 3b according to Paprosky, the implants could no longer be appropriately placed. The exterior form of the spherical implants tended to exhibit better coefficients than the conical/parabolic implants

New insights and research prospects from the ocean microbiome

Researchers with a certain amount of experience cannot help noticing the fast turnover of software tools and databases in the bioinformatics landscape. In order to thrive, metagenomic analysis and annotation tools have to remain up to date in terms of content, organization, and taxonomy; they have to be maintained by a devoted team of curators; and they should offer access and handles for a diverse and active user community that prevents them from falling into disuse. Finally, long-term institutional support is essential for staying power and longevity in this ever-changing field. The KAUST Metagenomic Analysis Platform (KMAP) appears among the latest entries within the field of large-scale metagenomic analysis and annotation. In their Frontiers in Science article, Laiolo and colleagues deliver an impressive rollout for the KMAP by assembling and analyzing an extensive global marine metagenome dataset, the Global Ocean Gene Catalog 1.0, which represents over 2,000 metagenomic samples predominantly from the open ocean and, to a smaller extent, from coastal waters and benthos. Numerous marine metagenomic samples from the European Nucleotide Archive (ENA; www.ebi.ac.uk/ena) were extracted as of May 2018 for processing in the KMAP, which includes quality control of readings and assembly of metagenomes. The large volume of this marine gene survey imposes some limits on the level of phylogenetic and functional detail that can be accommodated in a paper of reasonable length; therefore, this study emphasizes broad occurrence patterns of microbial classes and phyla, and major metabolic pathways

Microbial hydrocarbon degradation in Guaymas Basin—exploring the roles and potential interactions of fungi and sulfate-reducing bacteria

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Edgcomb, V., Teske, A., & Mara, P. Microbial hydrocarbon degradation in Guaymas Basin—exploring the roles and potential interactions of fungi and sulfate-reducing bacteria. Frontiers in Microbiology, 13, (2022): 831828, https://doi.org/10.3389/fmicb.2022.831828.Hydrocarbons are degraded by specialized types of bacteria, archaea, and fungi. Their occurrence in marine hydrocarbon seeps and sediments prompted a study of their role and their potential interactions, using the hydrocarbon-rich hydrothermal sediments of Guaymas Basin in the Gulf of California as a model system. This sedimented vent site is characterized by localized hydrothermal circulation that introduces seawater sulfate into methane- and hydrocarbon-rich sediments, and thus selects for diverse hydrocarbon-degrading communities of which methane, alkane- and aromatics-oxidizing sulfate-reducing bacteria and archaea have been especially well-studied. Current molecular and cultivation surveys are detecting diverse fungi in Guaymas Basin hydrothermal sediments, and draw attention to possible fungal-bacterial interactions. In this Hypothesis and Theory article, we report on background, recent results and outcomes, and underlying hypotheses that guide current experiments on this topic in the Edgcomb and Teske labs in 2021, and that we will revisit during our ongoing investigations of bacterial, archaeal, and fungal communities in the deep sedimentary subsurface of Guaymas Basin.This project was supported by collaborative NSF Biological Oceanography grants OCE-1829903 and OCE-1829680 “Hydrothermal fungi in the Guaymas Basin Hydrocarbon Ecosystem” to VE and AT, and collaborative NSF Biological Oceanography grants OCE-2046799 and OCE-2048489 “IODP-enabled Insights into Fungi and Their Metabolic Interactions with Other Microorganisms in Deep Subsurface Hydrothermal Sediments” to VE and AT. PM was supported by OCE-2046799 and OCE-1829903. Sampling in Guaymas Basin was supported by collaborative NSF Biological Oceanography grant 1357238 “Collaborative Research: Microbial carbon cycling and its interaction with sulfur and nitrogen transformations in Guaymas Basin hydrothermal sediments” to AT

Enrichment of Fusobacteria in Sea Surface Oil Slicks from the Deepwater Horizon Oil Spill

The Deepwater Horizon (DWH) oil spill led to rapid microbial community shifts in the Gulf of Mexico, including the formation of unprecedented quantities of marine oil snow (MOS) and of a massive subsurface oil plume. The major taxa that bloomed in sea surface oil slicks during the spill included Cycloclasticus, and to a lesser extent Halomonas, Alteromonas, and Pseudoalteromonas—organisms that grow and degrade oil hydrocarbons aerobically. Here, we show that sea surface oil slicks at DWH contained obligate and facultative anaerobic taxa, including members of the obligate anaerobic phylum Fusobacteria that are commonly found in marine sediment environments. Pyrosequencing analysis revealed that Fusobacteria were strongly selected for when sea surface oil slicks were allowed to develop anaerobically. These organisms have been found in oil-contaminated sediments in the Gulf of Mexico, in deep marine oil reservoirs, and other oil-contaminated sites, suggesting they have putative hydrocarbon-degrading qualities. The occurrence and strong selection for Fusobacteria in a lab-based incubation of a sea surface oil slick sample collected during the spill suggests that these organisms may have become enriched in anaerobic zones of suspended particulates, such as MOS. Whilst the formation and rapid sinking of MOS is recognised as an important mechanism by which a proportion of the Macondo oil had been transported to the sea floor, its role in potentially transporting microorganisms, including oil-degraders, from the upper reaches of the water column to the seafloor should be considered. The presence of Fusobacteria on the sea surface—a highly oxygenated environment—is intriguing, and may be explained by the vertical upsurge of oil that provided a carrier to transport these organisms from anaerobic/micro-aerophilic zones in the oil plume or seabed to the upper reaches of the water column. We also propose that the formation of rapidly-sinking MOS may have re-transported these, and other microbial taxa, to the sediment in the Gulf of Mexico

Deep subsurface microbiology : a guide to the research topic papers

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 4 (2013): 122, doi:10.3389/fmicb.2013.00122.Deep subsurface microbiology is a rising field in geomicrobiology, environmental microbiology and microbial ecology that focuses on the molecular detection and quantification, cultivation, biogeographic examination, and distribution of bacteria, archaea, and eukarya that permeate the subsurface biosphere. The deep biosphere includes a variety of subsurface habitats, such as terrestrial deep aquifer systems or mines, deeply buried hydrocarbon reservoirs, marine sediments and the basaltic ocean crust. The deep subsurface biosphere abounds with uncultured, only recently discovered and—at best—incompletely understood microbial populations. So far, microbial cells and DNA remain detectable at sediment depths of more than 1 km and life appears limited mostly by heat in the deep subsurface. Severe energy limitation, either as electron acceptor or donor shortage, and scarcity of microbially degradable organic carbon sources are among the evolutionary pressures that may shape the genomic and physiological repertoire of the deep subsurface biosphere. Its biogeochemical importance in long-term carbon sequestration, subsurface elemental cycling and crustal aging, is a major focus of current research at the interface of microbiology, geochemistry, and biosphere/geosphere evolution

Cultivation-dependent and cultivation-independent characterization of hydrocarbon-degrading bacteria in Guaymas Basin sediments

Marine hydrocarbon-degrading bacteria perform a fundamental role in the biodegradation of crude oil and its petrochemical derivatives in coastal and open ocean environments. However, there is a paucity of knowledge on the diversity and function of these organisms in deep-sea sediment. Here we used stable-isotope probing (SIP), a valuable tool to link the phylogeny and function of targeted microbial groups, to investigate polycyclic aromatic hydrocarbon (PAH)-degrading bacteria under aerobic conditions in sediments from Guaymas Basin with uniformly labeled [13C]phenanthrene. The dominant sequences in clone libraries constructed from 13C-enriched bacterial DNA (from phenanthrene enrichments) were identified to belong to the genus Cycloclasticus. We used quantitative PCR primers targeting the 16S rRNA gene of the SIP-identified Cycloclasticus to determine their abundance in sediment incubations amended with unlabeled phenanthrene and showed substantial increases in gene abundance during the experiments. We also isolated a strain, BG-2, representing the SIP-identified Cycloclasticus sequence (99.9% 16S rRNA gene sequence identity), and used this strain to provide direct evidence of phenanthrene degradation and mineralization. In addition, we isolated Halomonas, Thalassospira and Lutibacterium spp. with demonstrable phenanthrene-degrading capacity from Guaymas Basin sediment. This study demonstrates the value of coupling SIP with cultivation methods to identify and expand on the known diversity of PAH-degrading bacteria in the deep-sea

Deep-marine brine seeps stimulate microbial nitrogen cycling : implications for the formation of sediment-hosted ore deposits

Funding: This work was financially supported by a NERC Frontiers Grant (NE/V010824/1) and a Leverhulme Trust Grant (RPG‐2022‐ 313) to EES.Deep-marine brine seeps in the modern ocean are considered analogs for settings that favored the formation of sedimentary-exhalative zinc and lead deposits in deep time. Microbial activity plays an important role in the accumulation of ore minerals, meaning that the extent of mineralization is at least indirectly dependent on nutrient fluxes. Here, we investigated the biogeochemical nitrogen cycle in shallow (15–50 cm) sediment cores from the Orca Basin brine pool and surrounding sites, as well as from an active brine seep area near Dead Crab Lake in the Gulf of Mexico, with the aim of constraining the effect of brine seepage on this bio-essential element. We find high porewater ammonium concentrations in the millimolar range, paired with elevated ratios of organic carbon to nitrogen in sediments, which confirm previous hypotheses that the brine recycles ammonium from sedimentary strata back into the water column. Within Orca Basin, we note tentative evidence of microbial ammonium utilization. At the active seep, ammonium is mixed into the overlying water column and likely undergoes oxidation. Isotopic data from sediments and dissolved ammonium, paired with previously published genomic data, suggest the presence of dissimilatory nitrate reduction to ammonium at the brine-seawater interface. We conclude that brine seeps can stimulate biological nitrogen metabolisms in multiple ways. Our results may help calibrate studies of biogeochemical cycles around brine seeps that are archived in the rock record.Peer reviewe

How Clonal Is Clonal? Genome Plasticity across Multicellular Segments of a “Candidatus Marithrix sp.” Filament from Sulfidic, Briny Seafloor Sediments in the Gulf of Mexico

"Candidatus Marithrix" is a recently described lineage within the group of large sulfur bacteria (Beggiatoaceae, Gammaproteobacteria). This group of bacteria comprises vacuolated, attached-living filaments that inhabit the sediment surface around vent and seep sites in the marine environment. A single filament is ca. 100 µm in diameter, several millimeters long, and consists of hundreds of clonal cells, which are considered highly polyploid. Based on these characteristics, "Candidatus Marithrix" was used as a model organism for the assessment of genomic plasticity along segments of a single filament using next generation sequencing to possibly identify hotspots of microevolution. Using six consecutive segments of a single filament sampled from a mud volcano in the Gulf of Mexico, we recovered ca. 90% of the "Candidatus Marithrix" genome in each segment. There was a high level of genome conservation along the filament with average nucleotide identities between 99.98-100%. Different approaches to assemble all reads into a complete consensus genome could not fill the gaps. Each of the six segment datasets encoded merely a few hundred unique nucleotides and 5 or less unique genes - the residual content was redundant in all datasets. Besides the overall high genomic identity, we identified a similar number of single nucleotide polymorphisms (SNPs) between the clonal segments, which are comparable to numbers reported for other clonal organisms. An increase of SNPs with greater distance of filament segments was not observed. The polyploidy of the cells was apparent when analyzing the heterogeneity of reads within a segment. Here, a strong increase in single nucleotide variants, or 'intrasegmental sequence heterogeneity' (ISH) events, was observed. These sites may represent hotspots for genome plasticity, and possibly microevolution, since two thirds of these variants were not co-localized across the genome copies of the multicellular filament