Editorial: Hydrothermal microbial ecosystems

The papers in the “Hydrothermal Vent” research topic cover a range of microbiological research in deep and shallow hydrothermal environments, from high temperature “blacksmokers”, to diffuse flow habitats and episodically discharging subsurface fluids, to the hydrothermal plumes.Together they provide a snapshot of current research interests in a field that has evolved rapidly since the discovery of hydrothermal vents in 1977

Editorial: Hydrothermal microbial ecosystems

The papers in the “Hydrothermal Vent” research topic cover a range of microbiological research in deep and shallow hydrothermal environments, from high temperature “blacksmokers”, to diffuse flow habitats and episodically discharging subsurface fluids, to the hydrothermal plumes.Together they provide a snapshot of current research interests in a field that has evolved rapidly since the discovery of hydrothermal vents in 1977

Antibacterial Gene Transfer Across the Tree of Life

Though horizontal gene transfer (HGT) is widespread, genes and taxa experience biased rates of transferability. Curiously, independent transmission of homologous DNA to archaea, bacteria, eukaryotes, and viruses is extremely rare and often defies ecological and functional explanations. Here, we demonstrate that a bacterial lysozyme family integrated independently in all domains of life across diverse environments, generating the only glycosyl hydrolase 25 muramidases in plants and archaea. During coculture of a hydrothermal vent archaeon with a bacterial competitor, muramidase transcription is upregulated. Moreover, recombinant lysozyme exhibits broad-spectrum antibacterial action in a dose-dependent manner. Similar to bacterial transfer of antibiotic resistance genes, transfer of a potent antibacterial gene across the universal tree seemingly bestows a niche-transcending adaptation that trumps the barriers against parallel HGT to all domains. The discoveries also comprise the first characterization of an antibacterial gene in archaea and support the pursuit of antibiotics in this underexplored group

Editorial: Archaea in the Environment: Views on Archaeal Distribution, Activity, and Biogeography

On the occasion of the 10-year anniversary of Frontiers in Microbiology, this Research Topic was launched to highlight the linkages between extreme and archaeal microbiology (Teske, 2020). Archaea adapt to the physical and chemical characteristics of their habitat—such as organic matter availability, electron donor redox status, salinity, temperature, and pH—in terms of metabolic activity, community composition, gene expression patterns, and evolutionary diversification (Baker et al., 2020). Here, cultivation- and genome-based studies highlight linkages between archaea and their habitats (Figure 1)

Links from mantle to microbe at the Lau Integrated Study Site : insights from a back-arc spreading center

Author Posting. © The Oceanography Society, 2012. This article is posted here by permission of The Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 25, no. 1 (2012): 62–77, doi:10.5670/oceanog.2012.04.The Lau Integrated Study Site (ISS) has provided unique opportunities for study of ridge processes because of its back-arc setting in the southwestern Pacific. Its location allows study of a biogeographical province distinct from those of eastern Pacific and mid-Atlantic ridges, and crustal compositions along the ridge lie outside the range of mid-ocean ridge crustal compositions. The Lau ISS is located above a subduction zone, at an oblique angle. The underlying mantle receives water and other elements derived from the downgoing lithospheric slab, with an increase in slab influence from north to south. Water lowers the mantle melting temperature and leads to greater melt production where the water flux is greater, and to distinctive regional-scale gradients along the ridge. There are deeper faulted axial valleys with basaltic volcanism in the north and inflated axial highs with andesites in the south. Differences in igneous rock composition and release of magmatic volatiles affect compositions of vent fluids and deposits. Differences in vent fluid compositions and small-scale diffuse-flow regimes correlate with regional-scale patterns in microbial and megafaunal distributions. The interdisciplinary research effort at the Lau ISS has successfully identified linkages between subsurface processes and deep-sea biological communities, from mantle to microbe to megafauna.Support was provided by National Science Foundation grants OCE-1038135 to MKT, OCE-0732369 and OCE-0240985 to CRF, OCE-0732369 and OCE-0838107 to PRG, OCE-0242618 to CHL, OCE-0242902 and OCE-0752256 to PJM, OCE-0728391 and OCE-0937404 to A-LR, and a GRFP to RB

Genetics, Genomics and - Omics of Thermophiles

Thermophilic Archaea and Bacteria occupy heated environments. Advancement of next-generation sequencing (NGS), single-cell analyses, and combinations of –omics and microscopic technologies have resulted in the discovery of new thermophiles. This e-book consists of a review, and 10 original articles authored by 94 authors. The main aim of this Research Topic of Frontiers in Microbiology was to provide a platform for researchers to describe recent findings on the ecology of thermophiles using NGS, functional genomics, comparative genomics, gene evolution, and extremozyme discovery

New Opportunities and Untapped Scientific Potential in the Abyssal Ocean

The abyssal ocean covers more than half of the Earth’s surface, yet remains understudied and underappreciated. In this Perspectives article, we mark the occasion of the Deep Submergence Vehicle Alvin’s increased depth range (from 4500 to 6500 m) to highlight the scientific potential of the abyssal seafloor. From a geologic perspective, ultra-slow spreading mid-ocean ridges, Petit Spot volcanism, transform faults, and subduction zones put the full life cycle of oceanic crust on display in the abyss, revealing constructive and destructive forces over wide ranges in time and space. Geochemically, the abyssal pressure regime influences the solubility of constituents such as silica and carbonate, and extremely high-temperature fluid-rock reactions in the shallow subsurface lead to distinctive and potentially unique geochemical profiles. Microbial residents range from low-abundance, low-energy communities on the abyssal plains to fast growing thermophiles at hydrothermal vents. Given its spatial extent and position as an intermediate zone between coastal and deep hadal settings, the abyss represents a lynchpin in global-scale processes such as nutrient and energy flux, population structure, and biogeographic diversity. Taken together, the abyssal ocean contributes critical ecosystem services while facing acute and diffuse anthropogenic threats from deep-sea mining, pollution, and climate change

A comparison of taxon co-occurrence patterns for macro- and microorganisms

We examine co-occurrence patterns of microorganisms to evaluate community assembly “rules.” We use methods previously applied to macroorganisms, both to evaluate their applicability to microorganisms and to allow comparison of co-occurrence patterns observed in microorganisms to those found in macroorganisms. We use a null model analysis of 124 incidence matrices from microbial communities, including bacteria, archaea, fungi, and algae, and we compare these results to previously published findings from a meta-analysis of almost 100 macroorganism data sets. We show that assemblages of microorganisms demonstrate nonrandom patterns of co-occurrence that are broadly similar to those found in assemblages of macroorganisms. These results suggest that some taxon co-occurrence patterns may be general characteristics of communities of organisms from all domains of life. We also find that co-occurrence in microbial communities does not vary among taxonomic groups or habitat types. However, we find that the degree of co-occurrence does vary among studies that use different methods to survey microbial communities. Finally, we discuss the potential effects of the undersampling of microbial communities on our results, as well as processes that may contribute to nonrandom patterns of co-occurrence in both macrobial and microbial communities such as competition, habitat filtering, historical effects, and neutral processes