Acidimicrobiia, the actinomycetota of coastal marine sediments: Abundance, taxonomy and genomic potential

Microbial communities in marine sediments represent some of the densest and most diverse biological communities known, with up to a billion cells and thousands of species per milliliter. Among this taxonomic diversity, the class Acidimicrobiia, within the phylum Actinomycetota, stands out for its consistent presence, yet its limited taxonomic understanding obscures its ecological role. We used metagenome-assembled genomes from a 5-year Arctic fjord sampling campaign and compared them to publicly available Acidimicrobiia genomes using 16S rRNA gene and whole-genome phylogenies, alongside gene prediction and annotation to study their taxonomy and genomic potential. Overall, we provide a taxonomic overview of the class Acidimicrobiia and show its significant prevalence in Isfjorden and Helgoland coastal sediments, representing over 90% of Actinomycetota 16S rRNA gene sequences, and 3-7% of Bacteria. We propose Benthobacter isfjordensis gen. nov., sp. nov., Hadalibacter litoralis gen. nov., sp. nov., and two new species from Ilumatobacter, following SeqCode guidelines. In addition, we report the first in situ quantification of the family Ilumatobacteraceae, revealing its substantial presence (1-6%) in coastal sediments. This work highlights the need of refining the taxonomy of Acidimicrobiia to better understand their ecological contributions.

Unveiling the culturable and non-culturable actinobacterial diversity in two macroalgae species from the northern Portuguese coast

Actinomycetota, associated with macroalgae, remains one of the least explored marine niches. The secondary metabolism of Actinomycetota, the primary microbial source of compounds relevant to biotechnology, continues to drive research into the distribution, dynamics, and metabolome of these microorganisms. In this study, we employed a combination of traditional cultivation and metagenomic analysis to investigate the diversity of Actinomycetota in two native macroalgae species from the Portuguese coast. We obtained and taxonomically identified a collection of 380 strains, which were distributed across 12 orders, 15 families, and 25 genera affiliated with the Actinomycetia class, with Streptomyces making up approximately 60% of the composition. Metagenomic results revealed the presence of Actinomycetota in both Chondrus crispus and Codium tomentosum datasets, with relative abundances of 11% and 2%, respectively. This approach identified 12 orders, 16 families, and 17 genera affiliated with Actinomycetota, with minimal overlap with the cultivation results. Acidimicrobiales emerged as the dominant actinobacterial order in both macroalgae, although no strain affiliated with this taxonomic group was successfully isolated. Our findings suggest that macroalgae represent a hotspot for Actinomycetota. The synergistic use of both culture-dependent and independent approaches proved beneficial, enabling the identification and recovery of not only abundant but also rare taxonomic members.

Identification, classification, and functional characterization of novel sponge-associated acidimicrobiial species

Sponges are known to harbour an exceptional diversity of uncultured microorganisms, including members of the phylum Actinobacteriota. While members of the actinobacteriotal class Actinomycetia have been studied intensively due to their potential for secondary metabolite production, the sister class of Acidimicrobiia is often more abundant in sponges. However, the taxonomy, functions, and ecological roles of sponge-associated Acidimicrobiia are largely unknown. Here, we reconstructed and characterized 22 metagenome-assembled genomes (MAGs) of Acidimicrobiia from three sponge species. These MAGs represented six novel species, belonging to five genera, four families, and two orders, which are all uncharacterized (except the order Acidimicrobiales) and for which we propose nomenclature. These six uncultured species have either only been found in sponges and/or corals and have varying degrees of specificity to their host species. Functional gene profiling indicated that these six species shared a similar potential to non-symbiotic Acidimicrobiia with respect to amino acid biosynthesis and utilization of sulfur compounds. However, sponge-associated Acidimicrobiia differed from their non-symbiotic counterparts by relying predominantly on organic rather than inorganic sources of energy, and their predicted capacity to synthesise bioactive compounds or their precursors implicated in host defence. Additionally, the species possess the genetic capacity to degrade aromatic compounds that are frequently found in sponges. The novel Acidimicrobiia may also potentially mediate host development by modulating Hedgehog signalling and by the production of serotonin, which can affect host body contractions and digestion. These results highlight unique genomic and metabolic features of six new acidimicrobiial species that potentially support a sponge-associated lifestyle.

An enhanced excess sludge fermentation process by anthraquinone-2-sulfonate as electron shuttles for the biorefinery of zero-carbon hydrogen

Excess sludge (ES) largely produced in municipal wastewater treatment plants is known as a waste biomass and the traditional treatment processes such as landfill and incineration are considered as unsustainable due to the negative environmental impact. Fermentation process of ES for the biorefinery of zero-carbon hydrogen has attracted an increasing interesting and was extensively researched in the last decades. However, the technology is far from commercial application due to the insufficient effectivity. In the present study, anthraquinone-2-sulfonate (AQS) as electron shuttles was introduced into the fermentation process of ES for mediating the composition and activity of bacterial community to get an enhanced biohydrogen production. Inoculated with the same anaerobic activated sludge of 1.12 gVSS/L, a series of batch anaerobic fermentation systems with various dosage of AQS were conducted at the same ES load of 2.75 gVSS/L, initial pH 6.5 and 35 °C. The results showed that the fermentation process was remarkably enhanced by the introduction of 100 mg/L AQS, accompanying the lag phase was shortened to 1.35 h from 7.62. The obtained biohydrogen yield and the specific biohydrogen production rate were also remarkably enhanced to 24.9 mL/gVSS and 0.3 mL/(gVSS·h), respectively. Illumina Miseq sequencing showed that Longilinea and Guggenheimella as the dominant genera had been enriched from 9.2% to 0-12.0% and 4.7%, respectively, in the presence of 100 mg/L AQS. Function predicted analysis suggested that the presence of AQS had increased the abundance of genes involved in the transport and metabolism of carbohydrate, amino acid and energy production. Further redundancy analysis (RDA) revealed that the enhanced hydrogen production was highly positively correlated with the enrichment of genera such as Longilinea and Guggenheimella. The research work presents a novel potential biorefinery of ES for the effective production of zero-carbon hydrogen.

Rhabdothermincola salaria sp. nov., a novel actinobacterium isolated from a saline lake sediment

An actinobacterium, designated strain EGI L10124T, was isolated from saline lake sediment collected in Xinjiang province, PR China. The taxonomic position of the isolate was determined based on polyphasic taxonomic and phylogenomic analyses. Phylogenetic analysis and 16S rRNA gene sequence similarities indicated that strain EGI L10124T formed a distinct clade with Rhabdothermincola sediminis SYSU G02662T, with a shared sequence identity of 95.2 %. The novel isolate could be distinguished from species in the genus Rhabdothermincola by its distinct phenotypic, physiological and genotypic characteristics. The cells of strain EGI L10124T were aerobic, Gram-stain-positive and short rod-shaped. Optimal growth conditions of strain EGI L10124T on marine agar 2216 were registered at pH 8.0 at 37 °C. In addition, meso-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The major respiratory quinone was MK-9 (H8), while the major fatty acids were iso-C16 : 0, C17 : 0 and C16 : 0. The polar lipids included diphosphatidylglycerol, phosphatidylinositol mannoside and phosphatidylinositol. Based on the genome sequence of strain EGI L10124T, it appears that the G+C content of the novel isolate was 71.8 mol%. According to our data, strain EGI L10124T represents a new species of the genus Rhabdothermincola , for which the name Rhabdothermincola salaria sp. nov. is proposed. The type strain of the proposed novel isolate is EGI L10124T (=CGMCC 1.19113T=KCTC 49679T).

Influence of pipe material on biofilm microbial communities found in drinking water supply system

The biofilms and water samples from a model installation built of PVC-U, PE-HD and cast iron pipes were investigated using standard heterotrophic plate count and 16S rRNA Next Generation Sequencing. The results of the high throughput identification imply that the construction material strongly influences the microbiome composition. PVC-U and PE-HD pipes were dominated with Proteobacteria (54-60%) while the cast pipe was overgrown by Nitrospirae (64%). It was deduced that the plastic pipes create a more convenient environment for the potentially pathogenic taxa than the cast iron. The 7-year old biofilms were described as complex habitats with sharp oxidation-reduction gradients, where co-existence of methanogenic and methanotrophic microbiota takes place. Furthermore, it was found that the drinking water distribution systems (DWDS) are a useful tool for studying the ecology of rare bacterial phyla. New ecophysiological aspects were described for Aquihabitans, Thermogutta and Vampirovibrio. The discrepancy between identity of HPC-derived bacteria and NGS-revealed composition of biofilm and water microbiomes point to the need of introducing new diagnostical protocols to enable proper assessment of the drinking water safety, especially in DWDSs operating without disinfection.

Rhabdothermincola sediminis gen. nov., sp. nov., a new actinobacterium isolated from hot spring sediment, and emended description of the family Iamiaceae

One thermophilic bacterium, designated strain SYSU G02662^T, was isolated from hot spring sediment sampled in Tibet, PR China. Polyphasic taxonomic analyses and whole-genome sequencing were used to determine the taxonomy position of the strain. Phylogenetic analysis using 16S rRNA gene sequences indicated that strain SYSU G02662^T showed the highest sequence similarity to Actinomarinicola tropica SCSIO 58843^T (95.1 %). The strain could be differentiated from other species of the family Iamiaceae by its distinct phenotypic and genotypic characteristics. Cells of strain SYSU G02662^T were aerobic, Gram-staining-positive and short rodshaped. Growth occurred optimally at 45 °C and pH 7.0. In addition, meso-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The respiratory quinone was MK-9 (H₈), while the major fatty acids (>10 %) were C_16 : 0, C_17 : 0, C_18 : 0 and iso-C_16 : 0. The detected polar lipids included diphosphatidylglycerol, phosphatidylinositol mannoside and phosphatidylinositol. The G+C content of the genomic DNA was 70.5 % based on the draft genomic sequence. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU G02662^T represents a novel species of a novel genus in the family Iamiaceae, for which the name Rhabdothermincola sediminis gen. nov., sp. nov. is proposed. The type strain of the proposed novel species is SYSU G02662^T (=CGMCC 4.7688^T=KCTC 49500^T).

Distribution and diversity of filamentous bacteria in wastewater treatment plants exhibiting foaming of Taihu Lake Basin, China

Foaming caused by filamentous bacteria in activated sludge (AS) is a common phenomenon in municipal wastewater treatment plants (WWTPs) in Taihu Lake Basin of South China. In this study, total bacterial and filamentous bacterial communities were comprehensively characterized in AS and foams from eight municipal WWTPs by high-throughput sequencing technology. Results showed that alpha diversities of total bacterial communities in foams were obviously lower than those in AS samples. The bacterial community structures were significantly different between WWTPs rather than sample types (AS vs. foam). For most WWTPs, the Actinobacteria phylum was highly enriched in foams and the most abundant genera in foams were common mycolata. Sixteen filamentous bacteria were identified against the improved bulking and foaming bacteria (BFB) database. Abundance and composition of BFB in different WWTPs and different sample types were significantly different. 'Nostocoida limicola' I Trichococcus and Microthrix were generally dominant in AS samples. The dominant BFB in foams were associated with Microthrix, Skermania, Gordonia, and Mycobacterium. A new Defluviicoccus spp. in cluster III was identified in severe and continuous foams. Moreover, dominant BFB in stable and continuous foams with light level in one typical WWTP were diverse, even, and dynamic. Bacterial co-occurrence network analysis implied that the bacterial community of AS was more sensitive to disturbance than that of foam.

Applying constructed wetland-microbial electrochemical system to enhance NH4+ removal at low temperature

NH₄⁺ removal at low temperature (<10 °C) has baffled researchers and engineers for decades. Bioelectrochemical process has been increasingly valued as a promising approach to enhance NH₄⁺ removal by both electrochemical and stimulated microbial processes. The feasibility and the mechanism of enhanced NH₄⁺ removal were investigated in Constructed Wetland-Microbial Electrochemical System (CW-MES) with different electrode spacings including Constructed Wetland-Microbial Fuel Cell (CW-MFC) and Constructed Wetland-Microbial Electrolysis Cell (CW-MEC) at low temperature. Solar cell panel was firstly implemented in CW-MEC to enhance NH₄⁺ removal. The low-temperature operation lasted for about four months, CW-MEC successfully enhanced NH₄⁺ removal while CW-MFC did not exhibit positive effect. The NH₄⁺-N removal efficiency of CW-MEC achieved 88.2 ± 7.0%, which was 11.7 ± 6.5% higher than conventional constructed wetland (CCW). The maximum NH₄⁺-N removal efficiency of CW-MEC achieved 100%. The average NH₄⁺-N mass removal rate was 436.02 mg m^-2 d^-1. It was found that NH₄⁺ was mainly removed by the nitrification-autotrophic denitrification process in CW-MES while it was mainly converted to NO₃^- in CCW. Ammoxidation and denitrification were both enhanced by electricity while NH₄⁺ was used as the main substrate for electricity generation. AOA (Candidatus Nitrosocosmicus) and NOB (Nitrospira) were the main contributors to nitrification. This study provided a cost-effective and sustainable method for electrochemically enhanced microbial NH₄⁺ removal at low-temperature and revealed the relevant mechanism.

Desertimonas flava gen. nov., sp. nov. isolated from a desert soil, and proposal of Ilumatobacteraceae fam. nov

A non-motile, coccobacilli-shaped and yellow-coloured bacterium, designated strain SYSU D60003^T, was isolated from a desert soil sample. Cells were Gram-stain-positive, catalase-negative and oxidase-positive. The whole cell hydrolysates contained ll-diaminopimelic acid as the diagnostic amino acid. The major fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and iso-C16 : 0. The respiratory menaquinones were MK-9(H8), MK-9(H4) and MK-9(H6). The DNA G+C content was determined to be 70.2 % (genome). The polar lipids detected were diphosphatidylglycerol, an unidentified glycolipid and seven unidentified polar lipids. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SYSU D60003^T belonged to the order Acidimicrobiales (class Acidimicrobiia), but formed a clade closely linked to members of the genus Ilumatobacter. Data from a polyphasic taxonomy study suggested that the isolate represents a novel species of a novel genus in the order Acidimicrobiales, for which the name Desertimonas flava gen. nov., sp. nov. is proposed. The type strain of the proposed new taxon is SYSU D60003^T (=KCTC 39917^T=NBRC 112924^T). Additionally, the new taxon along with the genus Ilumatobater (family unassigned) were distinctly separated from the related families Acidimicrobiaceae, Iamiaceae and 'Microtrichaceae' in the phylogenetic trees, besides presenting a unique 16S rRNA gene signature nucleotides. Therefore, we propose a new family Ilumatobacteraceae fam. nov. within the order Acidimicrobiales to accommodate members of these two genera.

Comparison of Prokaryotic and Eukaryotic Communities in Soil Samples with and without Tomato Bacterial Wilt Collected from Different Fields

Biocontrol agents (BCA) effectively suppress soil-borne disease symptoms using natural antagonistic prokaryotes or eukaryotes. The main issue associated with the application of BCA is that disease reduction effects are unstable under different field conditions. In order to identify potentially effective BCA among several fields, we compared prokaryotic and eukaryotic communities in soil with and without tomato bacterial wilt from three different fields, each of which had the same field management and similar soil characteristics. Soil samples were collected from three fields and two depths because bacterial wilt pathogens were present in soil at a depth greater than 40 cm. We classified soil samples based on the presence or absence of the bacterial phcA gene, a key gene for bacterial wilt pathogenicity and tomato disease symptoms. Pyrosequencing of the prokaryotic 16S rRNA gene and eukaryotic internal transcribed spacer region sequences showed that the diversity and richness of the communities mostly did not correlate with disease symptoms. Prokaryotic and eukaryotic community structures were affected more by regional differences than the appearance of disease. Several prokaryotes and eukaryotes were more abundant in soil that lacked disease symptoms, and eight prokaryotes and one eukaryote of this group were commonly detected among the three fields. Some of these taxa were not previously found in disease-suppressive soil. Our results suggest that several prokaryotes and eukaryotes control plant disease symptoms.

Korean indigenous bacterial species with valid names belonging to the phylum Actinobacteria

To understand the isolation and classification state of actinobacterial species with valid names for Korean indigenous isolates, isolation source, regional origin, and taxonomic affiliation of the isolates were studied. At the time of this writing, the phylum Actinobacteria consisted of only one class, Actinobacteria, including five subclasses, 10 orders, 56 families, and 330 genera. Moreover, new taxa of this phylum continue to be discovered. Korean actinobacterial species with a valid name has been reported from 1995 as Tsukamurella inchonensis isolated from a clinical specimen. In 1997, Streptomyces seoulensis was validated with the isolate from the natural Korean environment. Until Feb. 2016, 256 actinobacterial species with valid names originated from Korean territory were listed on LPSN. The species were affiliated with three subclasses (Acidimicrobidae, Actinobacteridae, and Rubrobacteridae), four orders (Acidimicrobiales, Actinomycetales, Bifidobacteriales, and Solirubrobacterales), 12 suborders, 36 families, and 93 genera. Most of the species belonged to the subclass Actinobacteridae, and almost of the members of this subclass were affiliated with the order Actinomycetales. A number of novel isolates belonged to the families Nocardioidaceae, Microbacteriaceae, Intrasporangiaceae, and Streptomycetaceae as well as the genera Nocardioides, Streptomyces, and Microbacterium. Twenty-six novel genera and one novel family, Motilibacteraceae, were created first with Korean indigenous isolates. Most of the Korean indigenous actionobacterial species were isolated from natural environments such as soil, seawater, tidal flat sediment, and fresh-water. A considerable number of species were isolated from artificial resources such as fermented foods, wastewater, compost, biofilm, and water-cooling systems or clinical specimens. Korean indigenous actinobacterial species were isolated from whole territory of Korea, and especially a large number of species were from Jeju, Gyeonggi, Jeonnam, Daejeon, and Chungnam. A large number of novel actinobacterial species continue to be discovered since the Korean government is encouraging the search for new bacterial species and researchers are endeavoring to find out novel strains from extreme or untapped environments.