Proceedings of the National Academy of Sciences


Publications
15

Global diversity of enterococci and description of 18 previously unknown species

Citation
Schwartzman et al. (2024). Proceedings of the National Academy of Sciences 121 (10)
Names
Enterococcus mansonii Enterococcus ikei Enterococcus myersii Enterococcus leclercqii Enterococcus ferrettii Enterococcus wittei Enterococcus courvalinii Enterococcus palustris Enterococcus dunnyi Enterococcus huntleyi Enterococcus mangumiae Enterococcus moelleringii Enterococcus murrayae Enterococcus testudinis Enterococcus lowellii Enterococcus willemsii Enterococcus lemimoniae Enterococcus clewellii Vagococcus giribetii
Abstract
Enterococci are gut microbes of most land animals. Likely appearing first in the guts of arthropods as they moved onto land, they diversified over hundreds of millions of years adapting to evolving hosts and host diets. Over 60 enterococcal species are now known. Two species, Enterococcus faecalis and Enterococcus faecium, are common constituents of the human microbiome. They are also now leading causes of multidrug-resistant hospital-

Heme auxotrophy in abundant aquatic microbial lineages

Citation
Kim et al. (2021). Proceedings of the National Academy of Sciences 118 (47)
Names
“Planktophila rubra” “Planktophila aquatilis”
Abstract
Significance Heme is essential for respiration. As a cofactor of cytochromes, heme functions as a main electron carrier in all respiratory electron transport chains. Therefore, it is natural to expect all respiring and free-living microorganisms to make heme. Against this expectation, here we show that the acI lineage, one of the most abundant bacterial groups in freshwater environments, is unable to biosynthesize heme and requires exogenous heme. Furthermore, we provide genomic eviden

Multiple energy sources and metabolic strategies sustain microbial diversity in Antarctic desert soils

Citation
Ortiz et al. (2021). Proceedings of the National Academy of Sciences 118 (45)
Names
“Ca. Aridivita willemsiae” “Ca. Aridivita” “Ca. Aridivitaceae” Ca. Aridivitales Ca. Aridivitia
Abstract
Significance Diverse microbial life has been detected in the cold desert soils of Antarctica once thought to be barren. Here, we provide metagenomic, biogeochemical, and culture-based evidence that Antarctic soil microorganisms are phylogenetically and functionally distinct from those in other soils and adopt various metabolic and ecological strategies. The most abundant community members are metabolically versatile aerobes that use ubiquitous atmospheric trace gases to potentially mee

Legume–microbiome interactions unlock mineral nutrients in regrowing tropical forests

Citation
Epihov et al. (2021). Proceedings of the National Academy of Sciences 118 (11)
Names
“Acidoferrum” “Acidiferrales”
Abstract
Significance Symbiotic dinitrogen (N 2 )-fixing trees fulfill a critical function in tropical forests by bringing in new nitrogen, yet it remains unclear how they overcome constraints by highly weathered, nutrient-poor tropical soils. We advance forest biogeochemistry and microbial ecology with the discovery from field trials in Panama that fast-growing N 2 -fixing trees in tropical forests exhibit accelerated mineral weather

Symbiosis between nanohaloarchaeon and haloarchaeon is based on utilization of different polysaccharides

Citation
La Cono et al. (2020). Proceedings of the National Academy of Sciences 117 (33)
Names
“Nanohalobiia” Ca. Nanohalobium constans “Nanohalobiales” “Nanohalobiaceae”
Abstract
Significance We report on cultivation and characterization of an association between Candidatus Nanohalobium constans and its host, the chitinotrophic haloarchaeon Halomicrobium LC1Hm, obtained from a crystallizer pond of marine solar salterns. High-quality nanohaloarchael genome sequence in conjunction with electron- and fluorescence microscopy, growth analysis, and proteomic and metabolomic data revealed mutually beneficial

On the evolution and physiology of cable bacteria

Citation
Kjeldsen et al. (2019). Proceedings of the National Academy of Sciences 116 (38)
Names
Electronema Electrothrix Electrothrix communis Ts Electrothrix arhusiensis Electronema aureum Ts
Abstract
Cable bacteria of the family Desulfobulbaceae form centimeter-long filaments comprising thousands of cells. They occur worldwide in the surface of aquatic sediments, where they connect sulfide oxidation with oxygen or nitrate reduction via long-distance electron transport. In the absence of pure cultures, we used single-filament genomics and metagenomics to retrieve draft genomes of 3 marine Candidatus Electrothrix and 1 freshwater Ca.

A high-throughput system to identify inhibitors of Candidatus Liberibacter asiaticus transcription regulators

Citation
Barnett et al. (2019). Proceedings of the National Academy of Sciences 116 (36)
Names
Ca. Liberibacter asiaticus
Abstract
Citrus greening disease, also known as huanglongbing (HLB), is the most devastating disease of Citrus worldwide. This incurable disease is caused primarily by the bacterium Candidatus Liberibacter asiaticus and spread by feeding of the Asian Citrus Psyllid, Diaphorina citri. Ca. L. asiaticus cannot be cultured; its growth is restricted to citrus phloem and the psyllid insect. Management of infected trees includes use of broad-spectrum antibiotics, which have disadvantages. Recent work has sought

Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens

Citation
Berghuis et al. (2019). Proceedings of the National Academy of Sciences 116 (11)
Names
Ca. Methanomethylicia Ca. Methanomethylicaceae Ca. Methanomethylicales “Methanohydrogenicus thermophilus” Ca. Methanohydrogenales
Abstract
Methanogenic archaea are major contributors to the global carbon cycle and were long thought to belong exclusively to the euryarchaeal phylum. Discovery of the methanogenesis gene cluster methyl-coenzyme M reductase (Mcr) in the Bathyarchaeota, and thereafter the Verstraetearchaeota, led to a paradigm shift, pushing back the evolutionary origin of methanogenesis to predate that of the Euryarchaeota. The methylotrophic methanogenesis found in the non-Euryarchaota distinguished itself from the pre

Genomic diversification of giant enteric symbionts reflects host dietary lifestyles

Citation
Ngugi et al. (2017). Proceedings of the National Academy of Sciences 114 (36)
Names
“Epulonipiscioides gigas” “Epulonipiscioides saccharophilum” “Epulonipiscium fischelsonii”
Abstract
Significance Gastrointestinal symbionts of organisms are important in the breakdown of food for the host, particularly for herbivores requiring exogenous enzymes to digest complex polysaccharides in their diet. However, their role in the digestion of algae in marine piscine herbivores remains unresolved. Here, we show that the diversity of food sources available to herbivorous surgeonfishes is directly linked with the genetic makeup of their enteric microbiota. Importantly

Origin of microbial biomineralization and magnetotaxis during the Archean

Citation
Lin et al. (2017). Proceedings of the National Academy of Sciences 114 (9)
Names
“Magnetominusculus”
Abstract
Significance A wide range of organisms sense Earth’s magnetic field for navigation. For some organisms, like magnetotactic bacteria, magnetic particles form inside cells and act like a compass. However, the origin of magnetotactic behavior remains a mystery. We report that magnetotaxis evolved in bacteria during the Archean, before or near the divergence between the Nitrospirae and Proteobacteria phyla, suggesting that magnet