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Biofertilisers comprised of plant growth promoting bacteria (PGPB) present a promising sustainable alternative to synthetic fertilisers. Bacteria which consistently colonise roots of specific plants across distinct environments, known as that plant’s core root microbiome, are particularly promising due to their colonisation competency. However, traditional, culture-based techniques can overlook promising PGPB which do not display commonly screened for plant growth promoting traits. Although numerous studies have isolated beneficial root bacteria, few have combined bacterial metabarcoding with culture-based techniques to identify novel biofertiliser candidates. In a two-pronged approach, 16S rRNA amplicon sequencing was used to define the core root microbiome of the model cereal plant, Brachypodium distachyon, grown in four distinct soils. From 7,042 amplicon sequence variants (ASVs) detected in root fractions, only 40 ASVs were common at a prevalence of 80%. Core ASVs primarily belonged to the class Alphaproteobacteria, with the remainder comprising Actinobacteria, Bacilli, Chloroflexia, Gammaproteobacteria and Negativicutes. Secondly, B. distachyon root-associated bacterial strains were isolated from plants grown in the aforementioned soils. Of 207 root-associated isolates, 10 were identified as members of the core root microbiome, with the majority not displaying commonly screened for plant growth promoting traits. However, in a semi-hydroponic system, a core Bacillus and Rhodococcus strain significantly increased B. distachyon shoot dry weight by 32.8% and 40.0%, respectively. Additionally, two core Bacillus strains significantly increased root dry weight by 79.7 and 52.3%. This study demonstrates the potential of incorporating additional criteria afforded by culture-independent methods to select for novel biofertiliser candidates which may be overlooked by culture-dependent techniques.

The effect of Pseudomonas aeruginosa ( P. aeruginosa ) on the phytoremediation efficiency of ryegrass on soil contaminated with nonylphenol (NP) and cadmium (Cd) was investigated by pot experiments. Pseudomonas aeruginosa application stimulated the adsorption of Cd by ryegrass and facilitated the biodegradation of NP in the soil. Exogenous P. aeruginosa inoculation increased the activities of urease, dehydrogenase, and polyphenol oxidase in the soil of the T4 treatment by 38.5%, 50.0%, and 56.5% compared to that of the T2 treatment, respectively. There was a significant positive correlation between the activities of dehydrogenase and polyphenol oxidase and the NP removal rate ( P  < 0.001). The relative abundances of beneficial microorganisms (such as Sphingomonas , Lysobacter , Streptomyces , Chloroflexia, Deltaproteobacteria, and Alphaproteobacteria) were increased as a result of P. aeruginosa inoculation. These microorganisms play important roles in nutrient cycling, Cd adsorption, and NP degradation. Additionally, P. aeruginosa was not the dominate bacterial species at the end of the experiment. According to this study, P. aeruginosa application improved the phytoremediation efficiency of ryegrass on soil contaminated with NP and Cd, with a minimal risk of alien microbial invasion.

The phylum Chloroflexota (formerly Chloroflexi) encompasses metabolically diverse bacteria that often have high prevalence in terrestrial and aquatic habitats, some even with biotechnological application. However, there is substantial disagreement in public databases which lineage should be considered a member of the phylum and at what taxonomic level. Here, we addressed these issues through extensive phylogenomic analyses. The analyses were based on a collection of >5000 Chloroflexota genomes and metagenome-assembled genomes (MAGs) from public databases, novel environmental sites, as well as newly generated MAGs from publicly available sequence reads via an improved binning approach incorporating covariance information. Based on calculated relative evolutionary divergence, we propose that Candidatus Dormibacterota should be listed as a class (i.e., Ca. Dormibacteria) within Chloroflexota together with the classes Anaerolineae, Chloroflexia, Dehalococcoidia, Ktedonobacteria, Ca. Limnocylindria, Thermomicrobia, and two other classes containing only uncultured members. All other Chloroflexota lineages previously listed at the class rank appear to be rather orders or families in the Anaerolineae and Dehalococcoidia, which contain the vast majority of genomes and exhibited the strongest phylogenetic radiation within the phylum. Furthermore, the study suggests that a common ecophysiological capability of members of the phylum is to successfully cope with low energy fluxes.

The soil organic carbon is associated with the plant quality and the microbial community structure. In the present study, carbon fertilizers were applied to paddy soil to elucidate the relationship between soil carbon and neutral aroma substances in both tobacco and soil microbiome by transcriptome sequencing and 16S rDNA-based analysis, respectively. Our results showed that (1) the increase in soil carbon content was closely correlated with the abundance of microorganisms belonging to two classes (which could potentially affect tobacco plants), namely Gammaproteobacteria and Chloroflexia, (2) soil carbon apparently affected tobacco neutral aroma substances, and (3) soil carbon improved neutral aroma substances by affecting the transcriptional processes of sesquiterpenoid and chlorophyll biosyntheses. These results suggest that increased soil carbon—especially active organic carbon—resulted in desirable improvements in aroma substances in tobacco leaves.

Soil bacteria are key components of the soil microbial community contributing to soil health. Nitrogen (N) fertilization is an important factor that affects soil microbial community and cereal production. This study aims to explore the impact of long-term N fertilization on soil bacterial diversity, nitrogen use efficiency (NUE), and the grain yield of wheat in the semiarid region of Loess Plateau, China. The field experiment was conducted from 2003 to 2018 including five N treatments: 0 (N0), 52.5 (N52.5), 105 (N105), 157.5 (N157.5), and 210 (N210) kg N ha

Acacia mangium (AM) and Pinus massoniana (PM) are widely planted in tropical regions, whereas their effects on soil microbial communities remain unclear. We did a comprehensive investigation of soil denitrifying bacterial communities in AM and PM monoculture plantations in Southern China based on the high throughput sequencing data of their functional genes: nirK, nirS, and nosZ. The average abundance of nosZ (1.3 × 107) was significantly higher than nirS (5.6 × 106) and nirK (4.9 × 105). Shannon estimator revealed a markedly higher α-diversity of nirS and nosZ communities in PM than in AM plantations. The AM and PM plantations were dominated by different nirS and nosZ taxa belonging to proteobacteria, actinobacteria, thermoleophilia, chloroflexia, and acidobacteria, while the dominant nirK taxa were mainly categorized into proteobacteria in both types of plantations. The structure of nirS and nosZ communities shifted substantially from AM to PM plantations with changes in soil moisture, NH4+, and microbial biomass nitrogen content. The species co-occurrence network of nirK community was better organized in a more modular manner compared to nirS and nosZ communities, and the network keystone species mostly occurred in PM plantations. These results indicated a highly species corporation of nirK community in response to environmental changes, especially in PM plantations. AM and PM plantations can form different soil denitrifying microbial communities via altering soil physicochemical properties, which may further affect soil N transformations.

‘Candidatus Chloroploca asiatica’ B7–9 and ‘Candidatus Viridilinea mediisalina’ Kir15-3F are mesophilic filamentous anoxygenic phototrophic bacteria from alkaline aquatic environments. Both bacteria became available in the last few years and only in stable enrichment culture. In this study, we report the draft genomic sequences of ‘Ca. Chloroploca asiatica’ B7–9 and ‘Ca. Viridilinea mediisalina’ Kir15-3F, which were assembled from metagenomes of their cultures with a fold coverage 86.3× and 163.8×, respectively. The B7–9 (5.8 Mb) and the Kir15-3F (5.6 Mb) draft genome harbors 4818 and 4595 predicted protein-coding genes, respectively. In this article, we analyzed the phylogeny of representatives of the Chloroflexineae suborder in view of the appearance of new genomic data. These data were used for the revision of earlier published group-specific conserved signature indels and for searching for novel signatures for taxons in the Chloroflexineae suborder.