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Alkaline, sulfidic, 4 to 53 million-year-old meteoric water emanating from a borehole intersecting quartzite-hosted fractures greater than 3.3 kilometer beneath the surface have supported a microbial community dominated by a bacterial species with Desulfotomaculum spp. and an archaeal species related to Methanobacterium spp. These geochemical setting and microbial communities are notably different from microbial ecosystems reported for shallower continental subsurface environments.

Until recently, microbiologists have relied on cultures to understand the microbial world. As a result, model organisms have been the focus of research into understanding Bacteria and Archaea at a molecular level. Diversity surveys and metagenomic sequencing have revealed that these model species are often present in low abundance in the environment; instead, there are microbial taxa that are cosmopolitan in nature. Due to the numerical dominance of these microorganisms and the size of their habitats, these lineages comprise mind-boggling population sizes upward of 1028 cells on the planet. Many of these dominant groups have cultured representatives and have been shown to be involved in mediating key processes in nature. Given their importance and the increasing need to understand changes due to climate change, we propose that members of Nitrosophaerota (Nitrosopumilus maritimus), SAR11 (Pelagibacter ubique), Hadesarchaeia, Bathyarchaeia, and others become models in the future. Abundance should not be the only measure of a good model system; there are other organisms that are well suited to advance our understanding of ecology and evolution. For example, the most well-studied symbiotic bacteria, like Buchnera, Aliivibrio, and Rhizobium, should be models for understanding host-associations. Also, there are organisms that hold new insights into major transitions in the evolution of life on the planet like the Asgard Archaea (Heimdallarchaeia). Innovations in a variety of in situ techniques have enabled us to circumvent culturing when studying everything from genetics to physiology. Our deepest understanding of microbiology and its impact on the planet will come from studying these microbes in nature. Laboratory-based studies must be grounded in nature, not the other way around. [ABSTRACT FROM AUTHOR]

Research has been conducted on the microbial small-subunit rRNAs. The distribution of these rRNAs in Lake Michigan offshore sediments has been investigated via molecular biological methods, and the results indicate that the nitrogen cycling in these sediments may have a seasonal component.

The analysis of near-complete population (composite) genomic sequences for coexisting acidophilic iron-oxidizing Leptospirillum group II and III bacteria (phylum Nitrospirae) and an extrachromosomal plasmid from a Richmnd Mine, Iron Mountain, Ca, acid mine drainage biofilm is presented. Both the bacterial groups are found to have genes for community-essential functions, including carbon fixation and biosynthesis of vitamins, fatty acids, and biopolymers and multiple pathways for osmotic protection.

Analysis of an 18S rRNA gene library from a subsurface iron and sulfur-oxidizing microbial community growing in highly acidic (pH < 0.9) runoff within the Richmond Mine at Iron Mountain in northern California is presented. A limited diversity of archaea, bacteria, and viruses observed in AMD environment suggested that the environmental pressures and interplay between the members of these sulfur-oxidizing microbial communities limit species diversity at all trophic levels.

An analysis of assembled random shotgun sequence data from a low-diversity, subsurface acid mine drainage (AMD) biofilm revealed a single nif operon. The single nif operon was found on a fragment belonging to a member of Leptospirillum group III a lineage in the Nitrospirae phylum with no cultivated representatives.

Characterization of the diversity of filamentous fungi and protists in the Richmond Mine at Iron Mountain, Calif by utilizing both beta-tubulin and 18S rRNA gene sequence phylogenetic analyses is reported. The development of 18S rRNA fungal probes helped in identifying and studying the distribution of lineages of morphologically indistinguishable fungi in environmental samples. Three isolates with 18s rRNA genes that are closely related to the Dothideomycetes clones were obtained and the name 'Acidomyces richmondensis' is suggested for the isolates on the basis of their genus-level phylogenetic divergence and environmental adaptation.

Research has been conducted on protist endosymbionts from the acid mine drainage. The authors have investigated these endosymbionts via the use of culture-independent approaches.

Metagenomics of marine sediments has uncovered a broad diversity of new uncultured taxa, and provided the insights into their metabolic capabilities. Here, we detected microbial lineages from a sediment core near the Jiulong methane reef of the northern South China Sea (at 1100 m depth). Assembly and binning of the metagenomes resulted in 11 genomes (>85% complete) that represented nine distinct phyla including candidate phyla TA06 and LCP-89, Lokiarchaeota, Heimdallarchaeota, and a newly described globally distributed phylum (B38). The genome of LCP-89 has pathways for nitrate, selenate and sulfate reduction, suggesting that they may be involved in mediating these important processes. The B38 is able to participate in the cycling of hydrogen and selenocompounds. Many of these uncultured microbes may also be capable of autotrophic CO2 fixation, as exemplified by identification of the Wood-Ljungdahl (W-L) pathway. The carbohydrate degradation, W-L pathway, Rnf-dependent energy conservation and Ni/Fe hydrogenases were detected in the transcriptomes of these novel members. Characterizations of these new lineages provide insights to the undescribed branches in the tree of life. IMPORTANCE Sedimentary microorganisms in the South China Sea (SCS) remain largely unknown, due to the complexity of sediment communities impacted by continent rifting and extension. Distinct geochemical environments may breed special microbial communities including microbes that are still enigmatic. Functional inference of their metabolisms and transcriptional activity provided the insights in the ecological roles and substrate-based interactivity of these uncultured Archaea and Bacteria. These microorganisms play different roles in utilizing inorganic carbon and scavenging diverse organic compounds to involve in deep-sea carbon cycle. The genomes recovered here contributed undescribed species to the tree of life and laid a foundation for future study on these novel phyla persisting in marginal sediments of the SCS. [ABSTRACT FROM AUTHOR]

Defining the antiviral efficacy of CD8 T cells is important for immunogen design, and yet most current assays do not measure the ability of responses to neutralize infectious virus. Here we show that human immunodeficiency virus (HIV)-specific cytotoxic T-lymphocyte (CTL) clones and cell lines derived from infected persons and targeting diverse epitopes differ by over 1,000-fold in their ability to retard infectious virus replication in autologous CD4 T cells during a 7-day period in vitro, despite comparable activity as assessed by gamma interferon (IFN-γ) enzyme-linked immunospot (ELISPOT) assay. Cell lines derived from peripheral blood mononuclear cells stimulated in vitro with peptides representing targeted Gag epitopes consistently neutralized HIV better than Env-specific lines from the same person, although ineffective inhibition of virus replication is not a universal characteristic of Env-specific responses at the clonal level. Gag-specific cell lines were of higher avidity than Env-specific lines, although avidity did not correlate with the ability of Gag- or Env-specific lines to contain HIV replication. The greatest inhibition was observed with cell lines restricted by the protective HLA alleles B*27 and B*57, but stimulation with targeted Gag epitopes resulted in greater inhibition than did stimulation with targeted Env epitopes even in non-B*27/B*57 subjects. These results assessing functional virus neutralization by HIV-specific CD8 T cells indicate that there are marked epitope- and allele-specific differences in virus neutralization by in vitro-expanded CD8 T cells, a finding not revealed by standard IFN-γ ELISPOT assay currently in use in vaccine trials, which may be of critical importance in immunogen design and testing of candidate AIDS vaccines. [ABSTRACT FROM AUTHOR]

DPANN archaea have characteristically small cells and unique genomes that were long overlooked in diversity surveys. Their reduced genomes often lack essential metabolic pathways, requiring symbiotic relationships with other archaeal and bacterial hosts for survival. Yet a long-standing question remains, what is the advantage of maintaining ultrasmall cells. A recent study by Zhang et al. examined genomes of DPANN archaea from marine oxygen deficient zones (ODZs) (I. H. Zhang, B. Borer, R. Zhao, S. Wilbert, et al., mBio 15:e02918-23, 2024, https://doi.org/10.1128/mbio.02918-23). Surprisingly, these genomes contain a broad array of metabolic pathways including genes predicted to be involved in nitrous oxide (N 2 O) reduction. However, N 2 O levels are likely too low in ODZs to make this metabolically feasible. Modeling co-localization of DPANN archaea (N 2 O consumers) with other larger cells (N 2 O producers) demonstrates that N 2 O uptake rates can be optimized by maximizing the producer-to-consumer size ratio and proximity of consumer cells to producers. This may explain why such a diversity of archaea maintain extremely small cell sizes., Competing Interests: The authors declare no conflict of interest.