Search Results (23)

Native maize varieties provide important information for counteracting the effects of climate change, which leads to agricultural drought. The native rhizospheric microbiota is an ecological niche that maintains a close relationship with the plant and helps mitigate the effects of drought on it. The objective of this study was to describe the composition and structure of the rhizospheric bacterial communities of the native Pepitilla maize plants under conditions of water stress. An experiment was conducted under greenhouse conditions with three irrigation regimes and a control with normal irrigation. The responses of the plants to drought and the rhizospheric bacterial microbiota were measured before, during, and after the drought. Bacterial diversity was analyzed from rhizospheric soil using massive sequencing of the 16S rRNA gene. The drought model applied in the experiment had a negative effect on the plants, affecting their physiological, morphological, and biochemical functions. Diversity analyses showed statistical differences between the conditions during and after the drought in most cases. A reduction and modification in bacterial abundance was observed during the drought condition across different taxonomic groups, the most representative being the phyla Actinobacteriota, Pseudomonadota, and Acidobacteriota; the families Acidobacteriaceae, Rhodanobacteraceae, Solirubrobacteraceae, Acidothermaceae, and Microbacteriaceae; and the genera Actinobacteria, Sphingomonas, Geodermatophilus, Conexibacter, and Acidothermus. It is worth noting that the taxa Actinobacteria and Proteobacteria, as well as the families Microbacteriaceae, Sphingomonadaceae, and Unclassified_Actinobacteria, were directly associated with the drought condition, as an increase in their relative abundance was observed. This information is very useful for understanding the relationship between certain taxa enriched during stress conditions and the physiology of maize plants. Full article

Background: The respiratory microbiota is pivotal in maintaining pulmonary health and modulating disease; however, the intricate interplay between smoking, lung cancer, and microbiome composition remains incompletely understood. Here, we characterized the lower respiratory tract microbiome in a Russian cohort of 297 individuals, comprising healthy subjects and lung cancer patients of different smoking statuses (current smokers, former smokers, and nonsmokers). Methods: Using next-generation sequencing of the 16S rRNA gene from unstimulated sputum samples, we identify distinct microbiota signatures linked to smoking and lung cancer. A PERMANOVA (Adonis) test and linear discriminant analysis effect size were used for statistical analysis of data. Results: In healthy individuals, smoking did not affect microbiome diversity but markedly altered its composition, characterized by an increase in Streptococcus and a reduction in Neisseria as well as other genera such as Fusobacterium, Alloprevotella, Capnocytophaga, and Zhouea. Healthy former smokers’ microbiota profiles closely resembled those of healthy nonsmokers. In lung cancer patients, microbiome diversity and composition were minimally impacted by smoking, possibly due to the dominant influence of tumor-microenvironment-related factors. Nevertheless, Neisseria abundance remained significantly lower in smokers across advanced-stage lung cancer. Lung cancer patients exhibited distinctive microbiota signatures, including enrichment of Flavobacteriia, Bacillales, and Pasteurellales and depletion of Alphaproteobacteria, Coriobacteriaceae, and Microbacteriaceae, irrespective of smoking status. Conclusions: Our findings emphasize the profound impact of smoking on healthy respiratory microbiota which may be masked by lung-cancer-related factors. These insights highlight the necessity of considering smoking status in microbiome studies to enhance the understanding of respiratory health and disease. Full article

The bacterial community in water from the Houston-toad captive assurance colony held at the Houston Zoo, TX, was used for comparison to the native pond bacterial composition by Ilumina-based 16S rRNA V3 amplicon sequencing. We analyzed composite sediment–water samples from native breeding ponds before and after the release of eggstrands, focusing on opportunistic pathogens of the genus Mycobacterium within the phylum Actinobacteria. Proximal native breeding ponds without headstarting were analyzed for comparison. Tank-water samples from holding facilities (NACQ, Rm1, Rm3, Rm4) showed similar bacterial profiles, with sequences identifying Proteobacteria (57.8 ± 6.2% of all reads), Bacteriodetes (28.1 ± 8.9% of all reads), and Firmicutes (4.1 ± 2.0% of all reads) generally accounting for more than 90% of all reads. Actinobacteria were identified in low abundance, accounting for 1.4 ± 1.1% of all reads, with Nocardiaceae being the most prominent group (54 to 75% of reads), followed by Microbacteriaceae (6 to 12%) and Mycobacteriaceae (1 to 3%). In the pond samples, Proteobacteria remained the most prominent phylum, comprising about 30% of all reads, though other phyla such as Acidobacteria, Actinobacteria, Bacteriodetes, Chloroflexi, Cyanobacteria, Firmicutes, Planctomycetes, Verrucomicrobia, and others were also well represented, ranging from 1% to 15%, with individual phyla peaking at specific sampling times. The prevalence of Actinobacteria sequences varied widely among ponds (<1 to 11% of all reads) and over time (10% and 1%). Most mycobacteria sequences retrieved from tank water were not detected in pond water. Thus, the potential introduction of opportunistic mycobacteria pathogens with tank water from holding facilities and eggstrands via headstarting does not seem to lead to the establishment of these bacteria in natal ponds. Full article

Kazakhstan’s rich biodiversity includes diverse apple populations, notably the wild apple tree (Malus sieversii) prized for traits like disease resistance and adaptability, potentially aiding breeding programs. Analyzing their microbiomes offers insights into bacterial diversity and how it influences apple tree development, making it a reliable method for understanding ecological interactions. In this research, 334 apple tree samples were collected from different mountain ranges in southeastern Kazakhstan. An analysis using nanopore-based 16S rRNA sequencing showed a distinct similarity in the microbiome compositions of samples from the Zhongar and Ile Alatau mountain ranges, with a predominance of Pseudomonadaceae, Enterobacteriaceae, and Microbacteriaceae. In contrast, samples from Ketmen ridge showed a higher prevalence of Enterobacteriaceae. Alongside the less represented Pseudomonadaceae family, in the Ketmen ridge region, bacteria of the Xanthomonadaceae, Alcaligenaceae, and Brucellaceae families were also present. Across all regions, beneficial plant-associated bacteria were identified, such as Pseudomonas veronii, Stenotrophomonas geniculata, and Kocuria rhizophila, potentially enhancing plant resilience. However, opportunistic phytopathogens were also detected, including Pseudomonas viridiflava and Serratia marcescens, particularly in the Ile Alatau region. These findings highlight the complex microbial interactions in M. sieversii, thus offering key insights into host—microbe relationships that can inform apple breeding and ecological preservation efforts. Full article

The psychrophilic aerobic heterotrophic bacterium, strain 1639^T, was isolated from the low-temperature Lake Untersee in Antarctica. The bacterium was Gram-positive, non-motile, yellow–green-pigmented, non-spore-forming, and a pleomorphic rod. Growth was observed at temperatures of 0–25 °C with an optimum at 10 °C. The strain used urea as a nitrogen source. The major fatty acids were i-C_16:0 (49.69%), ai-C_15:0 (17.59%), and C_16:1 branched (12.03%). Identified polar lipids were phosphatidylglycerols and a glycolipid. The respiratory quinone was determined to be MK-10. The genomic DNA G+C content was 68.03 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 1639^T was a member of the genus Cryobacterium, with the highest sequence similarity to C. arcticum SK1^T (98.4%), C. soli GCJ02^T (98.4%), C. lactosi Sr59^T (98.3%), C. zongtaii TMN-42^T (98.2%), and C. adonitolivorans RHLS22-1^T (98.1%). The ANI and the DNA–DNA hybridization estimate values between strain 1639^T and all type strains of species of the genus Cryobacterium were in the range of 84.3–87.8% and 20.5–40.3%, respectively. The combined genotypic and phenotypic data indicate that strain 1639^T represents a novel species within the genus Cryobacterium, for which the name Cryobacterium inferilacus sp. nov. is proposed with the type strain 1639^T (=KCTC 59142^T, =VKM Ac-2907^T, UQM 41460^T). Full article

The formation of mineral-protected organic carbon (MPOC) is a vital process for soil organic carbon (SOC) accumulation and stabilization, influenced by factors such as exogenous carbon (C) input and soil microorganisms. However, the dynamics of MPOC and soil microorganisms following exogenous C input, and the key microorganisms driving MPOC formation, remain poorly understood. To address this, we conducted exogenous C addition culture experiments to investigate changes in MPOC and soil microorganisms and identify the primary microorganisms influencing MPOC formation. We observed that the MPOC content in treated soils increased over time, ranging from 0.43 to 2.06 g kg⁻¹. MPOC showed a significant positive correlation with soil bacterial diversity and a significant negative correlation with fungal diversity. Soil samples contained 248 bacterial families and 189 fungal genera, with Oxalobacteraceae (7.42%) and unclassified_k__Fungi (24.82%) being the most abundant, respectively. Using FAPROTAX and FunGuild ecological function prediction methods, we analyzed soil bacteria and fungi functional profiles and abundances. We identified the main bacterial families influencing MPOC formation as Microbacteriaceae, Mycobacteriaceae, Pseudomonadaceae, Streptomycetaceae, and Xanthomonadaceae. The primary fungal genera were Cylindrocarpon, Leohumicola, Metarhizium, Neobulgaria, Neopestalotiopsis, Olpidium, and Tetracladium. These findings provide theoretical support for understanding microbial regulation mechanisms in soil C sequestration and emission reduction. Full article

Industrial farming is one of the main farming systems used for L. vannamei, and it is also the main direction of development in the future. To investigate the role of the bacterial community in nitrogen transformation in industrial L. vannamei farming systems, we studied the concentration of nitrogen compounds, the bacterial community using 16S rRNA sequencing, and nitrogen cycling genes’ abundance using absolute quantitative PCR in aquaculture water (using seawater (WD) and groundwater mixed with seawater (CY)) and analyzed the correlations between them using a person analysis. The results showed that the bacterial α-diversity index (ACE, Shannon, and Sobs) significantly changed during culture in WD but not in CY. Bacterial community species composition analysis and linear discriminant analysis effect size (LEfSe analysis) revealed that Cyanobiaceae and Microbacteriaceae were the dominant bacteria and biomarkers in WD. Vibrionaceae, Ateromonadaceae, Microbacteriaceae, Saprospiraceae, and Cryomorphaceae were the dominant bacteria and biomarkers in CY. A functional annotation of procaryotic taxa (FAPROTAX) analysis revealed that the bacterial community in WD exhibited a greater phototrophic activity at early culture stages, while at the same stage, CY exhibited strong nitrate reduction. A correlation analysis of nitrogen cycling genes and environmental factors revealed that napA, narG, ureC, amoA, and nirK were significantly correlated with the concentrations of total ammonia nitrogen (TAN), nitrite (NO₂⁻-N), nitrate (NO₃⁻-N), and total nitrogen (TN) in WD. In CY, amoA was positively correlated and napA and nirK were negatively correlated with TAN and TN concentrations. A correlation analysis between bacterial abundance and environmental factors revealed that Flavobacteriaceae, Saprospiraceae, Cryomorphaceae, Cyanobiaceae, Halieaceae, and Cyclobacteriaceae were significantly correlated with the concentrations of TAN and NO₂⁻-N. The above results indicated that the bacterial community in industrial shrimp farming systems changed under different conditions, with consequent changes in the abundance of genes being involved in the nitrogen cycle and in this biogeochemical process in the water. Our study facilitates further understanding of microbes and their functions in nitrogen cycling in industrial shrimp farming systems. Full article

To reduce pesticide pollution and promote sustainable agricultural development in China, we designed a pilot-scale biofilter system to treat residual imidacloprid wastewater in an orchard. The biofilter system demonstrated a high rate of removal of imidacloprid from the biodegradation wastewater, with removal rates from the outlet exceeding 99% at different concentrations of pesticides. Among environmental factors, imidacloprid concentration at the inlet and biomixture significantly affected the activity of imidacloprid-degrading bacteria. The dominant microbial communities during the stable operation of the biofilter system included Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes at the phylum level and Bacillus, Methylobacter, and unclassified_f__Microbacteriaceae at the genus level. In future initiatives to improve biofilter performance and applicability, increasing attention should be paid to the dominant microbial communities, the number of biofilter units, and important environmental factors. Orchard workers in China should improve the existing treatment of residual pesticide wastewater to mitigate agricultural non-point source pollution. Full article

Philaenus spumarius (Linnaeus, 1758) (Hemiptera, Aphrophoridae) was recently classified as a pest due to its ability to act as a vector of the phytopathogen Xylella fastidiosa. This insect has been reported to harbour several symbiotic bacteria that play essential roles in P. spumarius health and fitness. However, the factors driving bacterial assemblages remain largely unexplored. Here, the bacteriome associated with different organs (head, abdomen, and genitalia) of males and females of P. spumarius was characterized using culturally dependent and independent methods and compared in terms of diversity and composition. The bacteriome of P. spumarius is enriched in Proteobacteria, Bacteroidota, and Actinobacteria phyla, as well as in Candidatus Sulcia and Cutibacterium genera. The most frequent isolates were Curtobacterium, Pseudomonas, and Rhizobiaceae sp.1. Males display a more diverse bacterial community than females, but no differences in diversity were found in distinct organs. However, the organ shapes the bacteriome structure more than sex, with the Microbacteriaceae family revealing a high level of organ specificity and the Blattabacteriaceae family showing a high level of sex specificity. Several symbiotic bacterial genera were identified in P. spumarius for the first time, including Rhodococcus, Citrobacter, Halomonas, Streptomyces, and Providencia. Differences in the bacterial composition within P. spumarius organs and sexes suggest an adaptation of bacteria to particular insect tissues, potentially shaped by their significance in the life and overall fitness of P. spumarius. Although more research on the bacteria of P. spumarius interactions is needed, such knowledge could help to develop specific bacterial-based insect management strategies. Full article

Tomato is the main vegetable cultivated under soilless culture systems (SCSs); production of organic tomato under SCSs has increased due to consumer demands for healthier and environmentally friendly vegetables. However, organic tomato production under SCSs has been associated with low crop performance and fruit quality defects. These agricultural deficiencies could be linked to alterations in tomato plant microbiota; nonetheless, this issue has not been sufficiently addressed. Thus, the main goal of the present study was to characterize the rhizosphere and phyllosphere of tomato plants cultivated under conventional and organic SCSs. To accomplish this goal, tomato plants grown in commercial greenhouses under conventional or organic SCSs were tested at 8, 26, and 44 weeks after seedling transplantation. Substrate (n = 24), root (n = 24), and fruit (n = 24) composite samples were subjected to DNA extraction and high-throughput 16S rRNA gene sequencing. The present study revealed that the tomato core microbiota was predominantly constituted by Proteobacteria, Actinobacteria, and Firmicutes. Remarkably, six bacterial families, Bacillaceae, Microbacteriaceae, Nocardioidaceae, Pseudomonadaceae, Rhodobacteraceae, and Sphingomonadaceae, were shared among all substrate, rhizosphere, and fruit samples. Importantly, it was shown that plants under organic SCSs undergo a dysbiosis characterized by significant changes in the relative abundance of Bradyrhizobiaceae, Caulobacteraceae, Chitinophagaceae, Enterobacteriaceae, Erythrobacteraceae, Flavobacteriaceae, Nocardioidaceae, Rhodobacteraceae, and Streptomycetaceae. These results suggest that microbial alterations in substrates, roots, and fruits could be potential factors in contributing to the crop performance and fruit quality deficiencies observed in organic SCSs. Full article

Antibiotic treatment is regarded as an emergency measure to avoid disease occurrence of aquatic animals during metamorphosis in an aquaculture system, which is very common in hatcheries of bivalve mollusc larvae. However, it is still unclear how and to what extent the antibiotic addition affects the prokaryotic and eukaryotic microbial communities of marine bivalve larvae. We profiled the community compositions and dominant taxonomies of prokaryotic and eukaryotic microbiota of Kumamoto oyster (Crassostrea sikamea) larvae exposed to seawater with antibiotics in trace concentration. A total of 500,664 16S rRNA and 501,933 18S rRNA gene fragments were selected for classification, resulting in 714 prokaryotic Operational Taxonomic Units (OTUs) and 47 eukaryotic OTUs. Antibiotic exposure altered the structure of larval microbiome and increased the prokaryotic but decreased the eukaryotic microbial diversity. Larval microbiota was sensitive to antibiotics, as evidenced by alternation of the dominant bacterial phyla Proteobacteria, Bacteroidetes, Firmicutes, Chlamydiae, and Actinobacteria, and eukaryotic phyla Streptophyta, Cercozoa, Chlorophyta and Haptophyta. Similarly, a significant effect was observed at the family and genus level, especially the increased bacterial Devosiaceae, Microbacteriaceae, Halieaceae, Vibrionaceae families, and Devosia, Stappia and Vibrio genera, and eukaryotic Isochrysidaceae and TAGIRI1-linage family and Tisochrysis genus. These results indicate that antibiotic treatment may induce a shift in the larval microbiome, which may cause an unstable community structure and in turn affect the oyster health. Full article

COVID-19 is a severe respiratory disease threatening pregnant women, which increases the possibility of adverse pregnancy outcomes. Several recent studies have demonstrated the ability of SARS-CoV-2 to infect the mother enterocytes, disturbing the gut microbiota diversity. The aim of this study was to characterize the entero-mammary microbiota of women in the presence of the virus during delivery. Fifty mother–neonate pairs were included in a transversal descriptive work. The presence of SARS-CoV-2 RNA was detected in nasopharyngeal, mother rectal swabs (MRS) and neonate rectal swabs (NRS) collected from the pairs, and human colostrum (HC) samples collected from mothers. The microbiota diversity was characterized by high-throughput DNA sequencing of V3-16S rRNA gene libraries prepared from HC, MRS, and NRS. Data were analyzed with QIIME2 and R. Our results indicate that several bacterial taxa are highly abundant in MRS positive for SARS-CoV-2 RNA. These bacteria mostly belong to the Firmicutes phylum; for instance, the families Bifidobacteriaceae, Oscillospiraceae, and Microbacteriaceae have been previously associated with anti-inflammatory effects, which could explain the capability of women to overcome the infection. All samples, both positive and negative for SARS-CoV-2, featured a high abundance of the Firmicutes phylum. Further data analysis showed that nearly 20% of the bacterial diversity found in HC was also identified in MRS. Spearman correlation analysis highlighted that some genera of the Proteobacteria and Actinobacteria phyla were negatively correlated with MRS and NRS (p < 0.005). This study provides new insights into the gut microbiota of pregnant women and their potential association with a better outcome during SARS-CoV-2 infection. Full article

Rotting wood is inhabited by a large diversity of bacteria, fungi, and insects with complex environmental relationships. The aim of this work was to study the composition of the microbiota (bacteria and fungi) in decaying wood from a northwest Spanish forest as a source of industrially relevant microorganisms. The analyzed forest is situated in a well-defined biogeographic area combining Mediterranean and temperate macrobioclimates. Bacterial diversity, determined by metagenome analyses, was higher than fungal heterogeneity. However, a total of 194 different cultivable bacterial isolates (mainly Bacillaceae, Streptomycetaceae, Paenibacillaceae, and Microbacteriaceae) were obtained, in contrast to 343 fungal strains (mainly Aspergillaceae, Hypocreaceae, and Coniochaetaceae). Isolates traditionally known as secondary metabolite producers, such as Actinobacteria and members of the Penicillium genus, were screened for their antimicrobial activity by the detection of antibiotic biosynthetic clusters and competitive bioassays against fungi involved in wood decay. In addition, the ability of Penicillium isolates to degrade cellulose and release ferulic acid from wood was also examined. These results present decaying wood as an ecologically rich niche and a promising source of biotechnologically interesting microorganisms. Full article

In order to study the linkages between the crop straw decomposition rate and the change in soil biological properties after the straw returned to the soil with different iron (Fe²⁺) contents, a 180-day incubation experiment was performed to examine the decomposition of maize straw (MS) under three Fe²⁺ levels, i.e., 0, 0.3, and 1 mg g⁻¹. Enzyme activities regarding straw decomposition and microbial communities under 0 and 1 mg g⁻¹ Fe addition were also detected. The results showed that Fe²⁺ addition significantly inhibited MS decomposition. This was evidenced by the higher contents of hemicellulose, cellulose, and lignin in Fe²⁺ treatments on day 180. High-Fe addition (1 mg g⁻¹) decreased the activity of Laccase (Lac) by 71.82% compared with control on day 30. Furthermore, the principal coordinates analysis (PCoA) indicated that high-Fe mainly affected the bacterial community. In particular, it suppressed the relative abundance of Microbacteriaceae in phylum Actinomycota that, in turn, is a potential decomposer of crop straw by secreting lignocellulolytic enzymes. A high level of Fe²⁺ inhibited the decomposition of hemicellulose, cellulose, and lignin in MS by reducing the relative abundance of phylum Actinobacteria in bacteria and suppressing Lac activity. Our findings provide guidance for returning crop straws in soils with high-Fe content. Full article

The genus of Curtobacterium, belonging to the Microbacteriaceae family of the Actinomycetales order, includes economically significant pathogenic bacteria of soybeans and other agricultural crops. Thorough phylogenetic and full-genome analysis using the latest genomic data has demonstrated a complex and contradictory taxonomic picture within the group of organisms classified as the Curtobacterium species. Based on these data, it is possible to delineate about 50 new species and to reclassify a substantial part of the Curtobacterium strains. It is suggested that 53 strains, including most of the Curtobacterium flaccumfaciens pathovars, can compose a monophyletic group classified as C. flaccumfaciens. A genomic analysis using the most recent inventory of bacterial chromosomal and plasmid genomes deposited to GenBank confirmed the possible role of Microbacteriaceae plasmids in pathogenicity and demonstrated the existence of a group of related plasmids carrying virulence factors and possessing a gene distantly related to DNA polymerase found in bacteriophages and archaeal and eukaryotic viruses. A PCR diagnostic assay specific to the genus Curtobacterium was developed and tested. The presented results assist in the understanding of the evolutionary relations within the genus and can lay the foundation for further taxonomic updates. Full article