Search Results (17)

Biochar application and controlled irrigation (CI) enhance water conservation, lower emissions, and increase crop yields. However, the synergistic effects on the relationship between paddy soil microstructure and microbiome remain poorly understood. This study investigates the impact of different irrigation regimes and biochar applications on soil physicochemical properties, soil microstructure, and the composition and functions of soil microorganisms in paddy soil. The CA treatment (CI with 60 t/hm² biochar) showed higher abundances of Mycobacteriaceae, Streptomycetaceae, Comamonadaceae, and Nocardioidaceae than the CK treatment (CI without biochar), which was attributed to two main factors. First, CA increased the pore throat equivalent radius (EqR), throat surface area (SAR), total throat number (TTN), volume fraction (VF), and connected porosity (CP) by 1.47–9.61%, 7.50–25.21%, 41.55–45.99%, 61.12–73.04%, and 46.36–93.75%, respectively, thereby expanding microbial habitats and providing refuges for microorganisms. Second, CA increased the cation exchange capacity (CEC), mean weight diameter (MWD), soil organic carbon (SOC), and total nitrogen (TN) by 22.14–25.06%, 42.24–56.61%, 22.98–56.5%, and 9.41–87.83%, respectively, reinforcing soil structural stability and carbon storage, which promoted microbial community diversity. FK (flood irrigation without biochar) showed no significant correlations with these environmental factors. Compared to CK soil metabolites at Level 2 and Level 3, FK exhibited higher levels of the citrate cycle, indicating that changes in water and oxygen environments due to CI reduced soil organic matter decomposition and carbon cycle. CA and CK strongly correlated with the soil microstructure (VF, CP, TTN, SAR, EqR), and CA notably enhanced soil metabolites related to the synthesis and degradation of ketone bodies, suggesting that biochar can mitigate the adverse metabolomic effects of CI. These results indicate that biochar application in CI paddy fields highlights the critical role of soil microstructure in microbial composition and function and better supports soil sustainability. Full article

Antarctica has attracted increasing interest in understanding its microbial communities, metabolic potential, and as a source of microbial hydrolytic enzymes with industrial applications, for which advances in next-generation sequencing technologies have greatly facilitated the study of unculturable microorganisms. In this work, soils from seven sub-Antarctic islands and Union Glacier were studied using a whole-genome shotgun metagenomic approach. The main findings were that the microbial community at all sites was predominantly composed of the bacterial phyla Actinobacteria and Cyanobacteria, and the families Streptomycetaceae and Pseudonocardiaceae. Regarding the xenobiotic biodegradation and metabolism pathway, genes associated with benzoate, chloroalkane, chloroalkene, and styrene degradation were predominant. In addition, putative genes encoding industrial enzymes with predicted structural properties associated with improved activity at low temperatures were found, with catalases and malto-oligosyltrehalose trehalohydrolase being the most abundant. Overall, our results show similarities between soils from different Antarctic sites with respect to more abundant bacteria and metabolic pathways, especially at higher classification levels, regardless of their geographic location. Furthermore, our results strengthen the potential of Antarctic soils as a source of industrially relevant enzymes. 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

Pesticides play a critical role in pest management and agricultural productivity; however, their misuse or overuse can lead to adverse effects on human health and the environment, including impacts on ecosystems and contamination. Currently, neonicotinoids (NNIs) are the most widely used systemic insecticides and are questioned worldwide for their possible impacts on pollinators. After NNI application, a substantial portion is not absorbed by the plant and may accumulate in the soil, affecting the soil microbial community. In this review, we explore the main studies carried out either in the laboratory or in the field about this matter. The studies report that the application of NNIs affects soil microbial activity and can act on microbial communities differently due to their unique chemical properties, degradation in soil, soil type, effects on soil properties, and methods of application. NNIs alter the diversity, structure, and abundance of soil microbes, in some cases increasing or decreasing their representativeness in soil. Bacterial phyla like Pseudomonadota, Bacillota, Actinomycetota, and Nitrospirota increase after NNI exposure, just like the families Nitrosomonadaceae, Nitrososphaeraceae, Nitrospiraceae, Sphingomonadaceae, Streptomycetaceae, and Catenulisporaceae. At the bacterial genus level, Nitrospira was associated with a decrease in nitrification processes in soil. The bacterial genera Sphingomonas, Streptomyces, Catenulispora, Brevundimonas, Pedobacter, and Hydrogenophaga are related to NNI degradation after application. Microorganisms could minimize the impacts of NNIs in agricultural soil. Therefore, the use of bioinoculation as a bioremediation tool is explored as an alternative to contribute to agricultural sustainability. Full article

Candidatus Liberibacter asiaticus (CLas) is associated with Citrus Huanglongbing (HLB), a devastating disease in the US. Previously, we conducted a two-year-long monthly HLB survey by quantitative real-time PCR using root DNA fractions prepared from 112 field grapefruit trees grafted on sour orange rootstock. Approximately 10% of the trees remained CLas-free during the entire survey period. This study conducted 16S metagenomics using the time-series root DNA fractions, monthly prepared during twenty-four consecutive months, followed by microbial co-occurrence network analysis to investigate the microbial factors contributing to the CLas-free phenotype of the aforementioned trees. Based on the HLB status and the time when the trees were first diagnosed as CLas-positive during the survey, the samples were divided into four groups, Stage H (healthy), Stage I (early), II (mid), and III (late) samples. The 16S metagenomics data using Silva 16S database v132 revealed that HLB compromised the diversity of rhizosphere microbiota. At the phylum level, Actinobacteria and Proteobacteria were the predominant bacterial phyla, comprising >93% of total bacterial phyla, irrespective of HLB status. In addition, a temporal change in the rhizosphere microbe population was observed during a two-year-long survey, from which we confirmed that some bacterial families differently responded to HLB disease status. The clustering of the bacterial co-occurrence network data revealed the presence of a subnetwork composed of Streptomycetaceae and bacterial families with plant growth-promoting activity in Stage H and III samples. These data implicated that the Streptomycetaceae subnetwork may act as a functional unit against HLB. Full article

The increasing number of infections caused by antimicrobial multi-resistant microorganisms has led to the search for new microorganisms capable of producing novel antibiotics. This work proposes Streptomyces pakalii sp. nov. as a new member of the Streptomycetaceae family. The strain ENCB-J15 was isolated from the jungle soil in Palenque National Park, Chiapas, Mexico. The strain formed pale brown, dry, tough, and buried colonies in the agar with no diffusible pigment in GAE (glucose–asparagine–yeast extract) medium. Scanning electron micrographs showed typical mycelium with long chains of smooth and oval-shaped spores (3–10 m). The strain grew in all of the International Streptomyces Project (ISP)’s media at 28–37 °C with a pH of 6–9 and 0–10% NaCl. S. pakalii ENCB-J15 assimilated diverse carbon as well as organic and inorganic nitrogen sources. The strain also exhibited significant inhibitory activity against the prodigiosin synthesis of Serratia marcescens and the inhibition of the formation and destruction of biofilms of ESKAPE strains of Acinetobacter baumannii and Klebsiella pneumoniae. The draft genome sequencing of ENCB-J15 revealed a 7.6 Mb genome with a high G + C content (71.6%), 6833 total genes, and 6746 genes encoding putative proteins. A total of 26 accessory clusters of proteins associated with carbon sources and amino acid catabolism, DNA modification, and the antibiotic biosynthetic process were annotated. The 16S rRNA gene phylogeny, core-proteome phylogenomic tree, and virtual genome fingerprints support that S. pakalii ENCB-J15 is a new species related to Streptomyces badius and Streptomyces globisporus. Similarly, its average nucleotide identity (ANI) (96.4%), average amino acid identity (AAI) (96.06%), and virtual DNA–DNA hybridization (67.3%) provide evidence to recognize it as a new species. Comparative genomics revealed that S. pakalli and its closest related species maintain a well-conserved genomic synteny. This work proposes Streptomyces pakalii sp. nov. as a novel species that expresses anti-biofilm and anti-quorum sensing activities. Full article

Scallop visceral mass and mantle are aquatic byproducts and waste, but they have high contents of protein. In this study, scallop visceral mass and mantle were used as supplements in the diet of juvenile sea cucumber (A. japonicus) and their effects on the growth, fatty acid and amino acid compositions, the non-specific immune responses and the intestinal microflora of A. japonicus were investigated through a 40 d feeding experiment. The results showed that dietary supplementation of scallop visceral mass significantly accelerated the specific growth rate (SGR) of juvenile A. japonicus by 3 times within 20 days, and also raised the contents of ω-3 fatty acids including EPA and DHA and the ω-3/ω-6 ratio of the sea cucumber tissue, which is favorable to the health and commercial value of the sea cucumber. Furthermore, it was found that the supplementation of scallop visceral mass and mantle stimulated the expression of immune-related genes and enhanced the immune defense in A. japonicus. Scallop visceral mass and mantle supplementation also increased the microbial diversity and the abundance of beneficial microbes including Bifidobacteriaceae, Streptomycetaceae, Clostridiaceae and Rhizobiales in the gut of A. japonicus. This study reveals the beneficial effects of dietary supplementation of scallop visceral mass and mantle on the growth of juvenile A. japonicus, which might be a promising way to reutilize this scallop waste and raise its economic value. Full article

Natural products have long been used as a source of antimicrobial agents against various microorganisms. Actinobacteria are a group of bacteria best known to produce a wide variety of bioactive secondary metabolites, including many antimicrobial agents. In this study, four actinobacterial strains found in Singapore terrestrial soil were investigated as potential sources of new antimicrobial compounds. Large-scale cultivation, chemical, and biological investigation led to the isolation of a previously undescribed tetronomycin A (1) that demonstrated inhibitory activities against both Gram-positive bacteria Staphylococcus aureus (SA) and methicillin-resistant Staphylococcus aureus (MRSA) (i.e., MIC₉₀ of 2–4 μM and MBC₉₀ of 9–12 μM), and several known antimicrobial compounds, namely nonactin, monactin, dinactin, 4E-deacetylchromomycin A3, chromomycin A2, soyasaponin II, lysolipin I, tetronomycin, and naphthomevalin. Tetronomycin showed a two- to six-fold increase in antibacterial activity (i.e., MIC₉₀ and MBC₉₀ of 1–2 μM) as compared to tetronomycin A (1), indicating the presence of an oxy-methyl group at the C-27 position is important for antibacterial activity. 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

Marine-derived Streptomyces actinomycetes are one of the most important sources for the discovery of novel bioactive natural products. This study characterized the isolation, structural elucidation and biological activity evaluation of thirty compounds, including twelve previously undescribed compounds, namely hygrocins K–U (5–13, 17 and 18) and streptophenylpropanamide A (23), from the marine-associated actinomycete Streptomyces sp. ZZ1956. Structures of the isolated compounds were determined by a combination of extensive NMR spectroscopic analyses, HRESIMS data, the Mosher’s method, ECD calculations, single crystal X-ray diffraction and comparison with reported data. Hygrocins C (1), D (2), F (4), N (8), Q (11) and R (12), 2-acetamide-6-hydroxy-7-methyl-1,4-naphthoquinone (22), echoside C (27), echoside A (28) and 11,11′-O-dimethylelaiophylin (30) had antiproliferative activity (IC₅₀: 0.16–19.39 μM) against both human glioma U87MG and U251 cells with hygrocin C as the strongest active compound (IC₅₀: 0.16 and 0.35 μM, respectively). The analysis of the structure–activity relationship indicated that a small change in the structures of the naphthalenic ansamycins had significant influence on their antiglioma activities. Hygrocins N (8), O (9), R (12), T (17) and U (18), 2-amino-6-hydroxy-7-methyl-1,4-naphthoquinone (21), 2-acetamide-6-hydroxy-7-methyl-1,4-naphthoquinone (22), 3′-methoxy(1,1′,4′,1″-terphenyl)-2′,6′-diol (26), echoside C (27) and echoside A (28) showed antibacterial activity against methicillin-resistant Staphylococcus aureus and Escherichia coli with MIC values of 3–48 μg/mL. Full article

Plant secondary succession is a very effective approach for the rejuvenation of degraded ecosystems. In order to comprehend alterations and driving mechanisms of soil bacterial communities under secondary succession of old-field and reveal their subsequent impacts on the decomposition and accumulation of soil organic carbon (SOC) and nitrogen (SON), we investigated changes in soil bacterial communities following ~160 years of old-field succession on the Loess Plateau of China through analyses of quantitative polymerase chain reaction (qPCR) and Illumina MiSeq DNA sequencing of 16S rRNA genes. Our results revealed that subsequent to secondary succession of old-field, soil bacterial abundance progressively increased, while bacterial richness and diversity significantly decreased. Principal component analysis and Bray–Curtis similarity index showed that bacterial community composition gradually shifted following old-field succession. Specifically, the relative abundances of Proteobacteria, Rokubacteria, and Verrucomicrobia progressively increased, while Actinobacteria and Firmicutes slightly decreased following old-field succession. The most enriched of Proteobacteria (e.g., Rhizobiales, Xanthobacteraceae, Gammaproteobacteria, Bradyrhizobium, Rhizobiaceae, and Mesorhizobiur) were found in a climax forest, while Chloroflexi and Gemmatimonadetes had the lowest relative abundances. Further, the most enriched members of Actinobacteria, including Geodermatophilaceae, Frankiales, Blastococcus, Micrococcales, Micrococcacea, Propionibacteriales, Nocardioidaceae, Nocardioide, and Streptomycetaceae, were exhibited in the farmland stage. Our results suggested that secondary succession of old-field greatly modified soil bacterial communities via the transformation of soil nutrients levels, altering plant biomass and soil physiochemical properties. Soil bacterial community composition was transformed from oligotrophic groups to copiotrophic Proteobacteria following old-field succession, which may promote SOC and SON accumulation through increasing the utilization of labile organic carbon (C) and nitrogen (N), while decreasing decomposition of recalcitrant organic C and N from the early- to late-successional stages. 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

Soil actinomycetes explorations appear to be an efficient alternative as biofertilizers to optimize the use of phosphorus (P) resources and enhance plant growth. This research aimed to explore the distribution of actinomycetes isolated from four different rhizospheric Moroccan oat soils and to investigate their potential for P solubilization. The distribution of actinomycetes was significantly more abundant in Settat (9.68%), Tangier (7.38%), and Beni Mellal (6.87%) than in the Merchouch-Rabat (4.90%) region. A total of 235 actinomycete strains were isolated from all sites and tested for their ability to grow on a synthetic minimum medium (SMM) containing insoluble natural rock phosphate (RP) or synthetic tricalcium phosphate (TCP) as the unique P source. One hundred forty-three isolates (60.8%) had the ability to grow in the SMM with RP whereas only twenty-five isolates (17%) had the most active growth using the SMM with TCP. Eight isolates with the most active growth in solid SMM were selected for their P solubilization abilities in liquid SMM cultures. The highest amount of P solubilized was 163.8 µg/mL for RP and 110.27 µg/mL for TCP after 5 days of culture. The biosolubilization process of AM2, the most efficient RP and TCP solubilizing strain, probably implied the highest excretion of siderophore substances. Eight of these strains were shown to belong to the Streptomyces genus and one to the Promicromonospora genus. These findings bolster the phosphate biosolubilization abilities of actinomycetes and may participate in increasing agricultural yields in an eco-efficient and environmentally friendly manner. Full article

Revegetation by planting shrubs on moving sand dunes is widely used to control desertification in arid/semi-arid areas. The soil including microbial community can gradually be improved along with plantation development. The purposes of this study were (1) to investigate the responses of microbial communities involved in the mineralization of soil organic phosphorus (OP) and dissolution of inorganic P (IOP) in the development of sand-fixating plantation and (2) to discuss the interactions between P turnover microbial communities and soil properties. We assessed the compositions of soil phoD gene (one of the Pho regulons encoding alkaline phosphomonoesterases) and gcd gene (encoding glucose dehydrogenase) in microbial community by using high-throughput Illumina MiSeq sequencing in a chronosequence of Caragana microphylla plantations (0-, 10-, 20-, and 37-year plantations and a native C. microphylla shrub forest) in Horqin Sandy Land, Northeast China. Soil properties including soil nutrients, enzymatic activity, and P fractions were also determined. The abundance of phoD and gcd genes linearly increased with the plantation age. However, the diversity of soil phoD microbes was more abundant than that of gcd. The phoD gene abundance and the fractions of total OP and IOP were positively correlated with the activity of phosphomonoesterase. Actinobacteria and Streptomycetaceae were the dominant phoD taxa, while Proteobacteria and Rhizobiaceae were the dominant gcd taxa. Plantation development facilitated the progressive successions of soil phoD and gcd communities resulting from the increase in the abundance of dominant taxa. Total soil N, NH₄-N, and available K were the main factors affecting the structures of phoD and gcd communities, while pH was not significantly influencing factor in such arid and nutrient-poor sandy soil. Many phoD or gcd OTUs were classified into Rhizobium and Bradyrhizobium, suggesting the coupling relationship between soil P turnover and N fixation. Full article

The genus Streptacidiphilus represents a group of acidophilic actinobacteria within the family Streptomycetaceae, and currently encompasses 15 validly named species, which include five recent additions within the last two years. Considering the potential of the related genera within the family, namely Streptomyces and Kitasatospora, these relatively new members of the family can also be a promising source for novel secondary metabolites. At present, 15 genome data for 11 species from this genus are available, which can provide valuable information on their biology including the potential for metabolite production as well as enzymatic activities in comparison to the neighboring taxa. In this study, the genome sequences of 11 Streptacidiphilus species were subjected to the comparative analysis together with selected Streptomyces and Kitasatospora genomes. This study represents the first comprehensive comparative genomic analysis of the genus Streptacidiphilus. The results indicate that the genomes of Streptacidiphilus contained various secondary metabolite (SM) producing biosynthetic gene clusters (BGCs), some of them exclusively identified in Streptacidiphilus only. Several of these clusters may potentially code for SMs that may have a broad range of bioactivities, such as antibacterial, antifungal, antimalarial and antitumor activities. The biodegradation capabilities of Streptacidiphilus were also explored by investigating the hydrolytic enzymes for complex carbohydrates. Although all genomes were enriched with carbohydrate-active enzymes (CAZymes), their numbers in the genomes of some strains such as Streptacidiphilus carbonis NBRC 100919^T were higher as compared to well-known carbohydrate degrading organisms. These distinctive features of each Streptacidiphilus species make them interesting candidates for future studies with respect to their potential for SM production and enzymatic activities. Full article