Publications

4511

Biological nitrogen fixation plays a crucial role in the marine nitrogen cycle, impacting global marine productivity and related carbon fluxes. The strains were analyzed by gene annotation, growth conditions and phylogenetic analysis of 16S rRNA gene sequences.These two strains were isolated from the coastal sediment at Xiaoshi Island in Weihai, China. The strains were analyzed by gene annotation, growth conditions and phylogenetic analysis of 16S rRNA gene sequences. It was revealed that strains D04T and AATT contain a set of nif gene clusters responsible for nitrogen fixation. Cell are yellow-colored, Gram-stain-negative, facultatively anaerobic, and rod-shaped bacteria. The optimal growth conditions for strain D04T were found to be at 33 °C, pH 7.0, and in 2% (w/v) NaCl, while strain AATT prefers growth conditions at 33 °C, pH 6.5, and in 3% (w/v) NaCl. The highest similarity of strains D04T and AATT was to Saccharicrinis fermentans NBRC 15936T, with a similarity of 94.1% and 94.8%, respectively. The 16S rRNA gene sequence similarity between the two strains was 96.6%. These novel strains were found to represent new taxa of the Marinilabiliaceae family, and we propose the names Plebeiobacterium marinum gen. nov., sp. nov. and Plebeiobacterium sediminum sp. nov. with type strains D04T (MCCC 1H00493T = KCTC 92026T) and AATT (MCCC 1H00485T = KCTC 92028T), respectively. In this study, nitrogen fixation genes were predicted for 53 strains from the whole order Marinilabiliales and it was found that nitrogen fixation gene clusters were present in 26 strains. These gene clusters were found in every family in the order, highlighting that the presence of nitrogen-fixing gene clusters in the order is common. Nitrogen-fixing bacteria in sediments play an important role in various biogeochemical cycles. Thus, understanding the oceanic nitrogen cycle can provide insights into the energy flow of marine systems.

Abstract Na.no.pu.sil'lus. Gr. masc. n. nânos, a dwarf; L. masc. adj. pusillus, very small; N.L. masc. n. Nanopusillus, a very small member of the Nanoarchaeota . The genus Candidatus Nanopusillus is comprised of small coccoid cells (∼100–400 nm) that live epibiotically on the surface of archaeal hosts. The first described species, Candidatus Nanopusillus acidilobi, is an anaerobic, hyperthermophilic acidophile whose best growth is observed at 82°C, pH 3.6, cultivated from a hot spring in Yellowstone National Park. Ca . Nanopusillus acidilobi cells associate with the Crenarchaeota host organism Acidilobus sp. 7A. Archaeal flagella (archaella) have been predicted from the genome sequence and shown to be expressed in the proteome. A second putative species, Candidatus Nanopusillus massiliensis, was recently reported from human dental plaque and associates with the methanogen Methanobrevibacter oralis . The genome consists of a single scaffold which is highly fragmented by spans of ambiguous nucleotides, with 16S rRNA gene fragments from Bacteria . Both species have small genomes (∼0.6 Mb) encoding few biosynthetic genes and no apparent ATP synthase complex genes, suggesting that the nanoarchaeotes rely on their host for the production of major cellular precursors. DNA G + C content (mol%) : 24 (genome analysis). Type species : Candidatus Nanopusillus acidilobi Wurch et al. 2016. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Nanopusillus is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Nanobdellati / Nanobdellota / Nanobdellia / Nanobdellales / Nanobdellaceae / Candidatus Nanopusillus The genus Candidatus Nanopusillus can also be recovered in the Genome Taxonomy Database (GTDB) as g__Nanopusillus (version v220) ** . GTDB classification: d__Archaea / p__Nanoarchaeota / c__Nanoarchaeia / o__Nanoarchaeales / f__Nanopusillaceae / g__Nanopusillus * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776

Abstract In the ongoing debates about eukaryogenesis—the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors—members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes 1 . However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved 2–4 . Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea and as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree and species tree reconciliation approaches, we show that analogous to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared with other archaea. Finally, we infer that the last common ancestor of Asgard archaea was probably a thermophilic chemolithotroph and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and a platform for better understanding the emergence of cellular complexity in eukaryotic cells.

Abstract Na.no.clep'ta. Gr. masc. n. nânos, a dwarf; Gr. masc. n. kleptês, a thief; N.L. masc. n. Nanoclepta, a small thief, a small organism that steals from its host. The genus Candidatus Nanoclepta currently comprises a single species, Candidatus Nanoclepta minutus Ncl‐1, an anaerobic hyperthermophile (optimal growth observed from 80 to 85°C) cultivated from a New Zealand hot spring. Cells are ultra‐small cocci (∼200 nm) with archaeal flagella and are cultivated in near‐neutral pH conditions (pH ∼6.0). Like several other Nanoarchaeota , Ca . N. minutus cells are epibionts on the surface of a host from the Crenarchaeota . Although this symbiosis is obligate for Ca . N. minutus, the relationship is not required for the host, Zestosphaera tikiterensis NZ3 T , which can survive as a free‐living organism. Ca . N. minutus has a highly reduced genome (∼0.58 Mb) with minimal biosynthetic potential and no detected ATP synthase genes, and Ca . Nanoclepta cells likely rely on their host for many metabolic precursors. DNA G + C content (mol%) : 32.2 (genome analysis). Type species : Candidatus Nanoclepta minutus St. John et al. 2019a. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Nanoclepta is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Nanobdellati / Nanobdellota / Nanobdellia / Nanobdellales / Nanobdellaceae / Candidatus Nanoclepta The genus Candidatus Nanoclepta can also be recovered in the Genome Taxonomy Database (GTDB) as g__Nanoclepta (version v220) ** . GTDB classification: d__Archaea / p__Nanoarchaeota / c__Nanoarchaeia / o__Nanoarchaeales / f__Nanopusillaceae / g__Nanoclepta * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776

In this paper, a comprehensive overview of the ‘Candidatus Liberibacter solanacearum’ presence in Europe was provided. The analyzed findings revealed that, since the first appearance of this pathogen in Finland and Spain in 2008, it has spread to 13 new European countries. Therefore, ‘Ca. L. solanacearum’ has spread very quickly across the European continent, as evident from the emergence of new host plants within the Apiaceae, Urticaceae, and Polygonaceae families, as well as new haplotypes of this pathogen. Thus far, 5 of the 15 ‘Ca. L. solanacearum’ haplotypes determined across the globe have been confirmed in Europe (haplotypes C, D, E, U, and H). Fully competent ‘Ca. L. solanacearum’ vectors include Bactericera cockerelli, Trioza apicalis, and B. trigonica; however, only T. apicalis and B. trigonica are presently established in Europe and are very important for plants from the Apiaceae family in particular. Moreover, psyllid species such as B. tremblayi, T. urticae, and T. anthrisci have also been confirmed positive for ‘Ca. L. solanacearum’. Constant monitoring of its spread in the field (in both symptomatic and asymptomatic plants), use of sensitive molecular diagnostic techniques, and application of timely management strategies are, therefore, of utmost importance for the control of this destructive pathogen.

Citrus Huanglongbing (HLB) is one of the most destructive diseases of citrus plants caused by the obligate and phloem-limiting bacterium Candidatus Liberibacter asiaticus (Las). Reliable detection methods are important for successful control of the disease. This study was aimed to develop a rapid and user-friendly on-site detection system for Las using the TaqMan probe-based insulated isothermal polymerase chain reaction (iiPCR) assay. The Las-specific on-site detection system could be completed within one hour by simple DNA extraction coupled with a portable POCKIT device, which can perform PCR amplification and automatically provide qualitative results derived from fluorescence signals. The sensitivity of the TaqMan probe-iiPCR assay could be as low as single copy of Las, comparable to a real-time PCR method. Further testing of the field citrus samples showed 100% agreement between the TaqMan probe-iiPCR assay and the real-time PCR method, and the on-site detection system also demonstrated a great performance of Las detection. With high specificity and sensitivity, the on-site detection system developed in this study becomes a simple, rapid and powerful tool for detecting Las in fields.

ABSTRACT The phylum Gemmatimonadota comprises mainly uncultured microorganisms that inhabit different environments such as soils, freshwater lakes, marine sediments, sponges, or corals. Based on 16S rRNA gene studies, the group PAUC43f is one of the most frequently retrieved Gemmatimonadota in marine samples. However, its physiology and ecological roles are completely unknown since, to date, not a single PAUC43f isolate or metagenome-assembled genome (MAG) has been characterized. Here, we carried out a broad study of the distribution, abundance, ecotaxonomy, and metabolism of PAUC43f, for which we propose the name of Palauibacterales . This group was detected in 4,965 16S rRNA gene amplicon datasets, mainly from marine sediments, sponges, corals, soils, and lakes, reaching up to 34.3% relative abundance, which highlights its cosmopolitan character, mainly salt-related. The potential metabolic capabilities inferred from 52 Palauibacterales MAGs recovered from marine sediments, sponges, and saline soils suggested a facultative aerobic and chemoorganotrophic metabolism, although some members may also oxidize hydrogen. Some Palauibacterales species might also play an environmental role as N 2 O consumers as well as suppliers of serine and thiamine. When compared to the rest of the Gemmatimonadota phylum, the biosynthesis of thiamine was one of the key features of the Palauibacterales . Finally, we show that polysaccharide utilization loci (PUL) are widely distributed within the Gemmatimonadota so that they are not restricted to Bacteroidetes , as previously thought. Our results expand the knowledge about this cryptic phylum and provide new insights into the ecological roles of the Gemmatimonadota in the environment. IMPORTANCE Despite advances in molecular and sequencing techniques, there is still a plethora of unknown microorganisms with a relevant ecological role. In the last years, the mostly uncultured Gemmatimonadota phylum is attracting scientific interest because of its widespread distribution and abundance, but very little is known about its ecological role in the marine ecosystem. Here we analyze the global distribution and potential metabolism of the marine Gemmatimonadota group PAUC43f, for which we propose the name of Palauibacterales order. This group presents a saline-related character and a chemoorganoheterotrophic and facultatively aerobic metabolism, although some species might oxidize H 2 . Given that Palauibacterales is potentially able to synthesize thiamine, whose auxotrophy is the second most common in the marine environment, we propose Palauibacterales as a key thiamine supplier to the marine communities. This finding suggests that Gemmatimonadota could have a more relevant role in the marine environment than previously thought.