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Environmental Microbiology Jan 2022Brown root rot (BRR) caused by Phellinus noxius is a destructive tree disease in tropical and subtropical areas. To understand how BRR affects the composition of the...
Brown root rot (BRR) caused by Phellinus noxius is a destructive tree disease in tropical and subtropical areas. To understand how BRR affects the composition of the plant rhizoplane-enriched microbiota, the microbiomes within five root-associated compartments (i.e., bulk soil, old/young root rhizosphere soil, old/young root tissue) of Ficus trees naturally infected by P. noxius were investigated. The level of P. noxius infection was determined by quantitative PCR. Illumina sequencing of the internal transcribed spacer and 16S rRNA revealed that P. noxius infection caused a significant reduction in fungal diversity in the bulk soil, the old root rhizosphere soil, and the old root tissue. Interestingly, Cosmospora was the only fungal genus positively correlated with P. noxius. The abundance and composition of dominant bacterial taxa such as Actinomadura, Bacillus, Rhodoplanes, and Streptomyces differed between BRR-diseased and healthy samples. Furthermore, 838 isolates belonging to 26 fungal and 35 bacterial genera were isolated and tested for interactions with P. noxius. Antagonistic activities were observed for isolates of Bacillus, Pseudomonas, Aspergillus, Penicillium, and Trichoderma. Cellophane overlay and cellulose/lignin utilization assays suggested that Cosmospora could tolerate the secretions of P. noxius and that the degradation of lignin by P. noxius may create suitable conditions for Cosmorpora growth.
Topics: Basidiomycota; Ficus; Microbiota; Plant Diseases; Plant Roots; RNA, Ribosomal, 16S; Rhizosphere; Soil Microbiology; Trees; Trichoderma
PubMed: 34863027
DOI: 10.1111/1462-2920.15862 -
Frontiers in Plant Science 2022is an important medicinal plant in traditional Chinese medicine, its rhizome is rich of volatile secondary metabolites with medicinal values and is largely demanded in...
is an important medicinal plant in traditional Chinese medicine, its rhizome is rich of volatile secondary metabolites with medicinal values and is largely demanded in modern markets. Currently, supply of high-yield, high-quality is mainly achieved cultivation. Certain soil microbes can benefit plant growth, secondary metabolism and induce resistance to environmental stresses. Hence, studies on the effects of soil microbe communities and isolates microorganisms on is extremely meaningful for future application of microbes on cultivation. Here we investigated the effects of the inoculation with an entire soil microbial community on the growth, resistance to drought, and accumulation of major medicinal compounds (hinesol, β-eudesmol, atractylon and atractylodin) of . We analyzed the interaction between and the soil microbes at the phylum and genus levels under drought stress of different severities (inflicted by 0%, 10% and 25% PEG6000 treatments). Our results showed that inoculation with soil microbes promoted the growth, root biomass yield, medicinal compound accumulation, and rendered drought-resistant traits of , including relatively high root:shoot ratio and high root water content under drought. Moreover, our results suggested drought stress was more powerful than the selectivity of in shaping the root-associated microbial communities; also, the fungal communities had a stronger role than the bacterial communities in protecting from drought. Specific microbial clades that might have a role in protecting from drought stress were identified: at the genus level, the rhizospheric bacteria , and , and rhizospheric fungi , , and , the root endophytic bacteria , , and , and the root endophytic fungus were closely associated with under drought stress. Additionally, we acquired several endophytic , and strains and verified they had differential promoting effects on the medicinal compound accumulation in root. This study reports the interaction between and soil microbe communities under drought stress, and provides insights for improving the outcomes in farming applying microbe inoculation.
PubMed: 36531372
DOI: 10.3389/fpls.2022.1032480 -
The Science of the Total Environment Jun 2021This study aimed to disclose the bacterial diversity succession during the co-composting of manure and crop residues and to provide new insight into the role of...
This study aimed to disclose the bacterial diversity succession during the co-composting of manure and crop residues and to provide new insight into the role of community-level dormancy potential in diversity succession. Illumina sequencing and PICRUSt-estimated metagenomes were used for this purpose. The bacterial richness and phylogenetic diversity decreased in the early and middle stages of composting and were maintained to a stable status in the late stage. Both composting phases and raw materials impacted the aforementioned alpha diversity significantly, while the composting phases had a greater (80%-94%) impact than the raw materials (1%-18%). Bacterial beta-diversity succession exhibited selectivity as the composting proceeded, and the dominant taxa changed into salt- and heat-resistant genera such as Bacillus, Glycomyces, and Halocella. Meanwhile, Georgenia, Actinomadura, and Ruminofilibacter were identified as the dominant predictor taxa of bacterial community succession in composting. Roughly, the abundance of genes underlying dormancy strategies, including sporulation factors (spo0A gene), toxin-antitoxin systems (dinJ/yafP, mazF/E, hipA/O, and relA/E genes), and resuscitation-promoting factors (rpfC gene), increased as composting proceeded and reached the highest in the thermophilic or maturation phases. Co-occurring relationships between bacterial communities and genes underlying dormancy strategies in different composting phases comprised multiple associations dominated by positive edges (50%-97%). The stability in genes underlying dormancy strategies and aggregate dormancy potential had a positive linear correlation with that in bacterial beta diversity (R = 0.26-0.42; P < 0.05), but not related significantly to that in richness and phylogenetic diversity. This study highlighted the importance of understanding how community-level dormancy strategies mediated microbial succession in composting to better predict compost maturity and product quality.
Topics: Bacteria; Composting; Manure; Phylogeny; Soil
PubMed: 33571759
DOI: 10.1016/j.scitotenv.2021.145506 -
Environmental Science and Pollution... Feb 2021The keratin-degrading bacterium Actinomadura viridilutea DZ50 secretes a keratinase (KERDZ) with potential industrial interest. Here, the kerDZ gene was extracellularly...
The keratin-degrading bacterium Actinomadura viridilutea DZ50 secretes a keratinase (KERDZ) with potential industrial interest. Here, the kerDZ gene was extracellularly expressed in Escherichia coli BL21(DE3)pLysS using pTrc99A vector. The recombinant enzyme (rKERDZ) was purified and biochemically characterized. Results showed that the native and recombinant keratinases have similar biochemical characteristics. The conventional dehairing with lime and sodium sulfide degrades the hair to the extent that it cannot be recovered. Thus, these chemical processes become a major contributor to wastewater problem and create a lot of environmental concern. The complete dehairing was achieved with 2000 U/mL rKERDZ for 10 h at 40 °C. In fact, keratinase assisted dehairing entirely degraded chicken feather (45 mg) and removed wool/hair from rabbit, sheep, goat, or bovine' hides (1.6 kg) while preserving the collagen structure. The enzymatic process is the eco-friendly option that reduces biological (BOD) (50%) and chemical (COD) oxygen demands (60%) in leather processing. Consequently, the enzymatic hair removal process could solve the problem of post-treatments encountering the traditional leather processing. The enzymatic (rKERDZ) dehaired leather was analyzed by scanning electron microscopic (SEM) studies, which revealed similar fiber orientation and compactness compared with control sample. Those properties support that the rKERDZ enzyme-mediated process is greener to some extent than the traditional one.
Topics: Actinomadura; Actinomycetales; Animals; Cattle; Feathers; Peptide Hydrolases; Rabbits; Sheep
PubMed: 33159682
DOI: 10.1007/s11356-020-11371-1 -
Frontiers in Plant Science 2022Endophytic actinobacteria aid in plant development and disease resistance by boosting nutrient uptake or producing secondary metabolites. For the first time, we...
Endophytic actinobacteria aid in plant development and disease resistance by boosting nutrient uptake or producing secondary metabolites. For the first time, we investigated the culturable endophytic actinobacteria associated with ten epiphytic orchid species of Assam, India. 51 morphologically distinct actinobacteria were recovered from surface sterilized roots and leaves of orchids and characterized based on different PGP and antifungal traits. According to the 16S rRNA gene sequence, these isolates were divided into six families and eight genera, where was most abundant (n=29, 56.86%), followed by , , , , , , and . Regarding PGP characteristics, 25 (49.01%) isolates demonstrated phosphate solubilization in the range of 61.1±4.4 - 289.7±11.9 µg/ml, whereas 27 (52.94%) isolates biosynthesized IAA in the range of 4.0 ± 0.08 - 43.8 ± 0.2 µg/ml, and 35 (68.62%) isolates generated ammonia in the range of 0.9 ± 0.1 - 5.9 ± 0.2 µmol/ml. These isolates also produced extracellular enzymes, viz. protease (43.13%), cellulase (23.52%), pectinase (21.56%), ACC deaminase (27.45%), and chitinase (37.25%). Out of 51 isolates, 27 (52.94%) showed antagonism against at least one test phytopathogen. In molecular screening, most isolates with antifungal and chitinase producing traits revealed the presence of 18 family chitinase genes. Two actinobacterial endophytes, sp. VCLA3 and sp. RVRA7 were ranked as the best strains based on PGP and antifungal activity on bonitur scale. GC-MS examination of ethyl acetate extract of these potent strains displayed antimicrobial compound phenol, 2,4-bis-(1,1-dimethylethyl) as the major metabolite along with other antifungal and plant growth beneficial bioactive chemicals. SEM analysis of fungal pathogen (MTCC 4633) affected by sp. VCLA3 revealed significant destruction in the spore structure. An plant growth promotion experiment with VCLA3 and RVRA7 on chili plants exhibited statistically significant (p<0.05) improvements in all of the evaluated vegetative parameters compared to the control. Our research thus gives insight into the diversity, composition, and functional significance of endophytic actinobacteria associated with orchids. This research demonstrates that isolates with multiple plant development and broad-spectrum antifungal properties are beneficial for plant growth. They may provide a viable alternative to chemical fertilizers and pesticides and a sustainable solution for chemical inputs in agriculture.
PubMed: 36570961
DOI: 10.3389/fpls.2022.1058867 -
Frontiers in Microbiology 2022Applications of organomineral fertilizer (OMF) are important measures for developing organic agriculture in karst mountain areas. However, the influence of OMF on the...
INTRODUCTION
Applications of organomineral fertilizer (OMF) are important measures for developing organic agriculture in karst mountain areas. However, the influence of OMF on the structure and function of soil microbial diversity and their relationship with crop yield and quality are still unclear.
METHODS
Based on soil science, crop science, and high-throughput sequencing methods, we investigated the changes of rhizosphere soil microbial communities of under different fertilization measures. Then, the relationship between yield and quality with soil quality was analyzed.
RESULTS
The results showed that the addition of OMF increased the amount of total carbon and total potassium in soil. OF, especially OMF, improved yield and quality (e.g., panicle number per plant, main panicle length, and unsaturated fatty acid contents). Both OF and OMF treatments significantly increased the enrichment of beneficial microorganism (e.g., , , , , , and ). The symbiotic network analysis demonstrated that OMF strengthened the connection among the soil microbial communities, and the community composition became more stable. Redundancy analysis and structural equation modeling showed that the soil pH, available phosphorus, and available potassium were significantly correlated with soil microbial community diversity and yield and quality.
DISCUSSION
Our study confirmed that OMF could replace or common OF to improve soil fertility, crop yield and quality in karst mountain soils.
PubMed: 36504806
DOI: 10.3389/fmicb.2022.1058067 -
Chemistry (Weinheim An Der Bergstrasse,... Jun 2022In this study, we analyzed if Actinomadura sp. RB99 produces siderophores that that could be responsible for the antimicrobial activity observed in co-cultivation...
In this study, we analyzed if Actinomadura sp. RB99 produces siderophores that that could be responsible for the antimicrobial activity observed in co-cultivation studies. Dereplication of high-resolution tandem mass spectrometry (HRMS/MS) and global natural product social molecular networking platform (GNPS) analysis of fungus-bacterium co-cultures resulted in the identification of five madurastatin derivatives (A1, A2, E1, F, and G1), of which were four new derivatives. Chemical structures were unambiguously confirmed by HR-ESI-MS, 1D and 2D NMR experiments, as well as MS/MS data and their absolute structures were elucidated based on Marfey's analysis, DP4+ probability calculation and total synthesis. Structure analysis revealed that madurastatin E1 (2) contained a rare 4-imidazolidinone cyclic moiety and madurastatin A1 (5) was characterized as a Ga -complex. The function of madurastatins as siderophores was evaluated using the fungal pathogen Cryptococcus neoformans as model organism. Based on homology models, we identified the putative NRPS-based gene cluster region of the siderophores in Actinomadura sp. RB99.
Topics: Actinomadura; Animals; Isoptera; Magnetic Resonance Spectroscopy; Siderophores; Tandem Mass Spectrometry
PubMed: 35404539
DOI: 10.1002/chem.202200612 -
Frontiers in Microbiology 2023Diels et Gilg, commonly known as Sanyeqing (SYQ), is an important traditional Chinese medicine. The content of bioactive constituents varies in different cultivars of...
Diels et Gilg, commonly known as Sanyeqing (SYQ), is an important traditional Chinese medicine. The content of bioactive constituents varies in different cultivars of SYQ. In the plant growth related researches, rhizosphere microbiome has gained significant attention. However, the role of bacterial communities in the accumulation of metabolites in plants have not been investigated. Herein, the composition of bacterial communities in the rhizosphere soils and the metabolites profile of different SYQ cultivars' roots were analyzed. It was found that the composition of microbial communities varied in the rhizosphere soils of different SYQ cultivars. The high abundance of , and other bacteria was found to be associated with the metabolites profile of SYQ roots. The findings suggest that the upregulation of rutin and hesperetin may contribute to the high bioactive constituent in SYQ roots. These results provide better understanding of the metabolite accumulation pattern in SYQ, and also provide a solution for enhancing the quality of SYQ by application of suitable microbial consortia.
PubMed: 38163074
DOI: 10.3389/fmicb.2023.1292896 -
Journal of Genomics 2020sp. K4S16 (=NBRC 110471) is a producer of a novel tetronate polyether compound nonthmicin. Here, we report the draft genome sequence of this strain together with...
sp. K4S16 (=NBRC 110471) is a producer of a novel tetronate polyether compound nonthmicin. Here, we report the draft genome sequence of this strain together with features of the organism and assembly, annotation and analysis of the genome sequence. The 9.6 Mb genome of sp. K4S16 encoded 9,004 putative ORFs, of which 7,701 were assigned with COG categories. The genome contained four type-I polyketide synthase (PKS) gene clusters, two type-II PKS gene clusters, and three nonribosomal peptide synthetase (NRPS) gene clusters. Among the type-I PKS gene () clusters, a large cluster was annotated to be responsible for nonthmicin synthesis based on bioinformatic analyses. We also performed feeding experiments using labeled precursors and propose the biosynthetic pathway of nonthmicin.
PubMed: 32494308
DOI: 10.7150/jgen.44650 -
PeerJ 2021This study aimed to investigate cultivable actinomycetes associated with rare honey bee species in Thailand and their antagonistic activity against plant pathogenic...
This study aimed to investigate cultivable actinomycetes associated with rare honey bee species in Thailand and their antagonistic activity against plant pathogenic bacteria. Actinomycetes were selectively isolated from the black dwarf honey bee (). A total of 64 actinomycete isolates were obtained with as the predominant genus (84.4%) followed by (7.8%), (4.7%) and (3.1%). All isolates were screened for antimicrobial activity against pv. and pv. . Three isolates inhibited the growth of pv. during screening. The crude extracts of two isolates (ASC3-2 and ASC5-7P) had a minimum inhibitory concentration (MIC) of 128 mg Lagainst pv. . For isolate ACZ2-27, its crude extract showed stronger inhibitory effect with a lower MIC value of 64 mg L against pv. . These three active isolates were identified as members of the genus based on their 16S rRNA gene sequences. Phylogenetic analysis based on the maximum likelihood algorithm showed that isolate ACZ2-27, ASC3-2 and ASC5-7P were closely related to NBRC 13063 (99.71%), subsp. NBRC 12748 (100%) and NBRC 12811 (100%), respectively. In addition, representative isolates from non- groups were identified by 16S rRNA gene sequence analysis. High similarities were found with members of the genera and . Our study provides evidence of actinomycetes associated with the black dwarf honey bee including members of rare genera. Antimicrobial potential of these insect associated was also demonstrated especially the antibacterial activity against phytopathogenic bacteria.
PubMed: 34589300
DOI: 10.7717/peerj.12097