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Biology Nov 2023The efficiency of plant-growth-promoting rhizobacteria (PGPR) may not be consistently maintained under field conditions due to the influence of soil microbial...
The efficiency of plant-growth-promoting rhizobacteria (PGPR) may not be consistently maintained under field conditions due to the influence of soil microbial communities. The present study aims to investigate their impact on three PGPR-based biofertilizers in wheat. We used the PGPR sp. strain B2 (PB2), PB2 in co-inoculation with 4042 (Mix 2), or with sp. SSM-004 and sp. SSM-001 (Mix 3). Inoculation of PB2, Mix 2, and Mix 3 into non-sterile field soil had a positive effect on root and aboveground dry biomass, depending on the wheat cultivar. The efficiency of the PGPR was further confirmed by the protection they provided against , the causal agent of Septoria leaf blotch disease. PB2 exhibited protection of ≥37.8%, while Mix 2 showed ≥47.9% protection in the four cultivars tested. These results suggest that the interactions between PGPR and native soil microbial communities are crucial for promoting wheat growth and protection. Additionally, high-throughput sequencing of microbial communities conducted 7 days after PGPR inoculations revealed no negative effects of PB2, Mix 2, and Mix 3 on the soil microbial community structure. Interestingly, the presence of spp. appeared to mitigate the potential negative effect of PB2 on bacterial community and foster root colonization by other beneficial bacterial strains.
PubMed: 37998015
DOI: 10.3390/biology12111416 -
Microbiological Research Feb 2024Rice germination and seedlings' growth are crucial stages that influence crop establishment and productivity. These performances depend on several factors, including the...
Rice germination and seedlings' growth are crucial stages that influence crop establishment and productivity. These performances depend on several factors, including the abundance and diversity of seed microbial endophytes. Two popular rainfed rice varieties cultivated in Cameroon, NERICA 3 and NERICA 8, were used for investigating the seed-associated microbiome using the Illumina-based 16 S rRNA gene. Significant differences were observed in terms of richness index between normal and abnormal seedlings developed from sprouting seeds, although no significant species evenness index was assessed within either phenotype. Two hundred ninety-two bacterial amplicon sequence variants were identified in seed microbiome of the rice varieties, and principal coordinate analysis revealed that microbial communities formed two distinct clusters in normal and abnormal seedling phenotypes. Overall, 38 bacteria genera were identified, belonging to 6 main phyla. Furthermore, the core microbiome was defined, and the differential abundance of 28 bacteria genera was assessed. Based on the collected results, putative bacterial genera were directly correlated with the development of normal seedlings. For most genera that are recognised to include beneficial species, such as Brevundimonas, Sphingomonas, Exiguobacterium, Luteibacter, Microbacterium and Streptomyces, a significant increase of their relative abundance was found in normal seedlings. Additionally, in abnormal seedlings, we also observed an increased abundance of the genera Kosakonia and Paenibacillus, which might have controversial aspects (beneficial or pathogenic), together with the presence of some genera (Clostridium sensu stricto) that are commonly correlated to sick plants. The putative functional gene annotation revealed the higher abundance of genes related to the metabolic biosynthesis of soluble carbohydrates and starch, tryptophan, nucleotides and ABC transporters in normal seedlings. Data presented in this study may help in further understanding the importance of the seed endophyte microbiome for driving a correct development of rice plants at the early stages and to identify possible beneficial bacteria for technological applications aimed to increase seed quality and crop productivity.
Topics: Oryza; Seedlings; Microbiota; Phenotype; Bacteria; Seeds
PubMed: 37992468
DOI: 10.1016/j.micres.2023.127546 -
Microbiology Resource Announcements Dec 2023Discovered from soil in a flower planter in Pocatello, Idaho and using , SallyK is a lytic bacteriophage with a siphovirus morphology. It has a 62,883 bp-long genome...
Discovered from soil in a flower planter in Pocatello, Idaho and using , SallyK is a lytic bacteriophage with a siphovirus morphology. It has a 62,883 bp-long genome with 103 putative genes. Based on gene content similarity to actinobacteriophages, SallyK is assigned to cluster EG.
PubMed: 37991360
DOI: 10.1128/MRA.00943-23 -
Microbiology Resource Announcements Dec 2023Bacteriophage DumpQuist was isolated from soil collected in Clarksville, TN, using the bacterium . Electron microscopy revealed that DumpQuist has a podovirus...
Bacteriophage DumpQuist was isolated from soil collected in Clarksville, TN, using the bacterium . Electron microscopy revealed that DumpQuist has a podovirus morphology. DumpQuist has a 53,924-bp genome that contains 54 predicted protein-coding genes and is most similar to phages in actinobacteriophage cluster EK1.
PubMed: 37991355
DOI: 10.1128/MRA.00923-23 -
Animal Microbiome Nov 2023The goal of this study was to assess the microbial ecology and diversity present in the uterus of post-partum dairy cows with and without metritis from 24 commercial...
BACKGROUND
The goal of this study was to assess the microbial ecology and diversity present in the uterus of post-partum dairy cows with and without metritis from 24 commercial California dairy farms using shotgun metagenomics. A set subset of 95 intrauterine swab samples, taken from a larger selection of 307 individual cow samples previously collected, were examined for α and β diversity and differential abundance associated with metritis. Cows within 21 days post-partum were categorized into one of three clinical groups during sample collection: control (CT, n = 32), defined as cows with either no vaginal discharge or a clear, non-purulent mucus vaginal discharge; metritis (MET, n = 33), defined as a cow with watery, red or brown colored, and fetid vaginal discharge; and purulent discharge cows (PUS, n = 31), defined as a non-fetid purulent or mucopurulent vaginal discharge.
RESULTS
All three clinical groups (CT, MET, and PUS) were highly diverse, with the top 12 most abundant genera accounting for 10.3%, 8.8%, and 10.1% of mean relative abundance, respectively. The α diversity indices revealed a lower diversity from samples collected from MET and PUS when compared to CT cows. PERMANOVA statistical testing revealed a significant difference (P adjusted < 0.01) in the diversity of genera between CT and MET samples (R2 = 0.112, P = 0.003) and a non-significant difference between MET and PUS samples (R2 = 0.036, P = 0.046). ANCOM-BC analysis revealed that from the top 12 most abundant genera, seven genera were increased in the natural log fold change (LFC) of abundance in MET when compared to CT samples: Bacteroides, Clostridium, Fusobacterium, Phocaeicola, Porphyromonas, Prevotella, and Streptococcus. Two genera, Dietzia and Microbacterium, were decreased in natural LFC of abundance when comparing MET (regardless of treatment) and CT, while no changes in natural LFC of abundance were observed for Escherichia, Histophilus, and Trueperella.
CONCLUSIONS
The results presented here, are the current deepest shotgun metagenomic analyses conducted on the bovine uterine microbiome to date (mean of 256,425 genus-level reads per sample). Our findings support that uterine samples from cows without metritis (CT) had increased α-diversity but decreased β-diversity when compared to metritis or PUS cows, characteristic of dysbiosis. In summary, our findings highlight that MET cows have an increased abundance of Bacteroides, Porphyromonas, and Fusobacterium when compared to CT and PUS, and support the need for further studies to better understand their potential causal role in metritis pathogenesis.
PubMed: 37986012
DOI: 10.1186/s42523-023-00281-5 -
Microbiology Resource Announcements Dec 2023Bacteriophage Morrigan, which was isolated from soil using NRRL B-24224, is lytic with siphovirus morphology. Morrigan's 40,509-bp genome has a GC content of 62.8% and...
Bacteriophage Morrigan, which was isolated from soil using NRRL B-24224, is lytic with siphovirus morphology. Morrigan's 40,509-bp genome has a GC content of 62.8% and 66 putative protein-coding genes, of which 31 could be assigned putative functions. Based on gene content similarity to actinobacteriophages, Morrigan is assigned to subcluster EA6.
PubMed: 37975671
DOI: 10.1128/MRA.00719-23 -
Microbiology Resource Announcements Dec 2023We report here the draft genome sequences of ( = 1), ( = 1), ( =1), spp. ( = 5), ( = 3), and isolated from high-touch surfaces in washrooms at a post-secondary...
We report here the draft genome sequences of ( = 1), ( = 1), ( =1), spp. ( = 5), ( = 3), and isolated from high-touch surfaces in washrooms at a post-secondary institution.
PubMed: 37971276
DOI: 10.1128/MRA.00910-23 -
ISME Communications Nov 2023Identifying interspecies interactions in mixed-species biofilms is a key challenge in microbial ecology and is of paramount importance given that interactions govern...
Identifying interspecies interactions in mixed-species biofilms is a key challenge in microbial ecology and is of paramount importance given that interactions govern community functionality and stability. We previously reported a bacterial four-species biofilm model comprising Stenotrophomonas rhizophila, Bacillus licheniformis, Microbacterium lacticum, and Calidifontibacter indicus that were isolated from the surface of a dairy pasteuriser after cleaning and disinfection. These bacteria produced 3.13-fold more biofilm mass compared to the sum of biofilm masses in monoculture. The present study confirms that the observed community synergy results from dynamic social interactions, encompassing commensalism, exploitation, and amensalism. M. lacticum appears to be the keystone species as it increased the growth of all other species that led to the synergy in biofilm mass. Interactions among the other three species (in the absence of M. lacticum) also contributed towards the synergy in biofilm mass. Biofilm inducing effects of bacterial cell-free-supernatants were observed for some combinations, revealing the nature of the observed synergy, and addition of additional species to dual-species combinations confirmed the presence of higher-order interactions within the biofilm community. Our findings provide understanding of bacterial interactions in biofilms which can be used as an interaction-mediated approach for cultivating, engineering, and designing synthetic bacterial communities.
PubMed: 37968339
DOI: 10.1038/s43705-023-00328-3 -
Frontiers in Microbiology 2023Microbial colonization represents one of the main threats to the conservation of subterranean cultural heritage sites. Recently, the microbial colonization on murals in...
BACKGROUND
Microbial colonization represents one of the main threats to the conservation of subterranean cultural heritage sites. Recently, the microbial colonization on murals in tombs has gradually attracted attention.
METHODS
In this study, a total of 33 samples, including 27 aerosol samples and 6 mural painting samples, were collected from different sites of Xu Xianxiu's Tomb and analyzed using culture-dependent methods. We compared the diversities of culturable bacteria and fungi isolated from the air and murals and explored the potential impacts of microorganisms on the biodeterioration of the murals.
RESULTS
Phylogenetic analyses revealed that the culturable bacteria belonged to Bacillus, Microbacterium, Lysobacter and Arthrobacter. And the most of fungal belonged to the Penicillium, Cladosporium and Aspergillus genera. The composition and structure of airborne bacteria and fungi outside the tomb were both significantly different from that inside the tomb. The variation trends of airborne bacterial and fungal concentrations at different sampling sites were remarkably similar. Bacillus frigoritolerans, Bacillus halotolerans, Bacillus safensis, Exiguobacterium mexicanum, Microbacterium trichothecenolyticum, and Micrococcus yunnanensis were bacterial species commonly isolated from both the mural and air environments. Fungal species commonly isolated from aerosol samples and mural painting samples were Alternaria alternata, Cladosporium cladosporioides, Penicillium brevicompactum, and Peyronellaea glomerata. The prediction of the ecological functions of the bacteria revealed that chemoheterotrophy or aerobic_chemoheterotrophy accounted for substantial relative proportions in all sample types.
CONCLUSION
These results suggest that the aerosol circulation between the inside and outside environments of the tomb was weak and that the outside environment had yet to have an impact on the air microbial community inside the tomb. Selective colonization of microorganisms, which is mediated by interaction between microorganisms and special microenvironmental factors, is an important reason for the biodeterioration of murals.
PubMed: 37954248
DOI: 10.3389/fmicb.2023.1253461 -
Microbiology Resource Announcements Nov 2023We purified two novel bacteriophages from soil collected in Sioux County, Iowa: BAjuniper and Tedro. These bacteriophages were isolated from the host, . BAjuniper was...
We purified two novel bacteriophages from soil collected in Sioux County, Iowa: BAjuniper and Tedro. These bacteriophages were isolated from the host, . BAjuniper was assigned to cluster EB, and Tedro was assigned to cluster EF. Both phages display genomes typical of other phages in their clusters.
PubMed: 37905824
DOI: 10.1128/MRA.00793-23