Probst, Alexander J.


Publications
8

Differential expression of core metabolic functions inCandidatusAltiarchaeum inhabiting distinct subsurface ecosystems

Citation
Esser et al. (2023).
Names
Ca. Altiarchaea “Altiarchaeum” Ca. Altiarchaeum crystalense
Abstract
AbstractCandidatusAltiarchaea are widespread across aquatic subsurface ecosystems and possess a highly conserved core genome, yet adaptations of this core genome to different biotic and abiotic factors based on gene expression remain unknown. Here, we investigated the metatranscriptome of twoCa. Altiarchaeum populations that thrive in two substantially different subsurface ecosystems. In Crystal Geyser, a high-CO2groundwater system in the USA,Ca. Altiarchaeum crystalense co-occurs with the symbi

Genomic remnants of ancestral methanogenesis and hydrogenotrophy in Archaea drive anaerobic carbon cycling

Citation
Adam et al. (2022). Science Advances 8 (44)
Names
“Hecatellales” “Hecatella orcuttiae” “Hecatella” “Hecatellaceae”
Abstract
Anaerobic methane metabolism is among the hallmarks of Archaea, originating very early in their evolution. Here, we show that the ancestor of methane metabolizers was an autotrophic CO 2 -reducing hydrogenotrophic methanogen that possessed the two main complexes, methyl-CoM reductase (Mcr) and tetrahydromethanopterin-CoM methyltransferase (Mtr), the anaplerotic hydrogenases Eha and Ehb, and a set of other genes collectively called “methanogenesis markers” but

SeqCode: a nomenclatural code for prokaryotes described from sequence data

Citation
Hedlund et al. (2022). Nature Microbiology
Names
Kryptonium mobile Kryptoniaceae Kryptoniia Kryptoniales
Abstract
AbstractMost prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single-amplified genome sequences. Otherwise, it is s

Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface

Citation
Probst et al. (2018). Nature Microbiology 3 (3)
Names
“Moissliibacteriota” “Ratteibacteriota” “Saganiibacteriota” “Torokiibacteriota” “Altiarchaeota” “Altiarchaeia” “Altiarchaeales” “Altiarchaeaceae” “Altiarchaeum hamiconexum” “Altiarchaeum”
Abstract
AbstractAn enormous diversity of previously unknown bacteria and archaea has been discovered recently, yet their functional capacities and distributions in the terrestrial subsurface remain uncertain. Here, we continually sampled a CO2-driven geyser (Colorado Plateau, Utah, USA) over its 5-day eruption cycle to test the hypothesis that stratified, sandstone-hosted aquifers sampled over three phases of the eruption cycle have microbial communities that differ both in membership and function. Geno

Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO<sub>2</sub> concentrations

Citation
Probst et al. (2017). Environmental Microbiology 19 (2)
Names
“Desantisiibacteriota”
Abstract
SummaryAs in many deep underground environments, the microbial communities in subsurface high‐CO2 ecosystems remain relatively unexplored. Recent investigations based on single‐gene assays revealed a remarkable variety of organisms from little studied phyla in Crystal Geyser (Utah, USA), a site where deeply sourced CO2‐saturated fluids are erupted at the surface. To provide genomic resolution of the metabolisms of these organisms, we used a novel metagenomic approach to recover 227 high‐quality

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

Citation
Anantharaman et al. (2016). Nature Communications 7 (1)
Names
“Nealsoniibacteriota” “Niyogiibacteriota” “Portnoyibacteriota” “Raymondiibacteriota” “Ryaniibacteriota” “Schekmaniibacteriota” “Spechtiibacteriota” “Staskawicziibacteriota” “Sungiibacteriota” “Tagaibacteriota” “Tayloriibacteriota” “Terryibacteriota” “Vebleniibacteriota” “Yonathiibacteriota” “Zambryskiibacteriota” “Rifleibacteriota” “Ozemibacteria”
Abstract
AbstractThe subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth’s biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics to aquifer sediments and groundwater, and reconstruct 2,540 draft-quality, near-complete and complet

A new view of the tree of life

Citation
Hug et al. (2016). Nature Microbiology 1 (5)
Names
“Rokuibacteriota” “Abawacaibacteriota” “Wirthibacterota”
Abstract
AbstractThe tree of life is one of the most important organizing principles in biology1. Gene surveys suggest the existence of an enormous number of branches2, but even an approximation of the full scale of the tree has remained elusive. Recent depictions of the tree of life have focused either on the nature of deep evolutionary relationships3–5 or on the known, well-classified diversity of life with an emphasis on eukaryotes6. These approaches overlook the dramatic change in our understanding o