Nitrogen, phosphorus, and potassium are the three most essential micronutrients which play major roles in plant survivability by being a structural or non-structural component of the cell. Plants acquire these nutrients from soil in the fixed (NO3 ̄, NH4+) and solubilized forms (K+, H2PO4- and HPO42-). In soil, the fixed and solubilized forms of nutrients are unavailable or available in bare minimum amounts; therefore, agrochemicals were introduced. Agrochemicals, mined from the deposits or chemically prepared, have been widely used in the agricultural farms over the decades for the sake of higher production of the crops. The excessive use of agrochemicals has been found to be deleterious for humans, as well as the environment. In the environment, agrochemical usage resulted in soil acidification, disturbance of microbial ecology, and eutrophication of aquatic and terrestrial ecosystems. A solution to such devastating agro-input was found to be substituted by macronutrients-availing microbiomes. Macronutrients-availing microbiomes solubilize and fix the insoluble form of nutrients and convert them into soluble forms without causing any significant harm to the environment. Microbes convert the insoluble form to the soluble form of macronutrients (nitrogen, phosphorus, and potassium) through different mechanisms such as fixation, solubilization, and chelation. The microbiomes having capability of fixing and solubilizing nutrients contain some specific genes which have been reported in diverse microbial species surviving in different niches. In the present review, the biodiversity, mechanism of action, and genomics of different macronutrients-availing microbiomes are presented.
- MeSH
- Bacteria * metabolismus genetika klasifikace MeSH
- biodiverzita * MeSH
- biotechnologie * MeSH
- draslík metabolismus MeSH
- dusík metabolismus MeSH
- fosfor metabolismus MeSH
- mikrobiota * MeSH
- půda chemie MeSH
- půdní mikrobiologie MeSH
- zemědělské plodiny MeSH
- zemědělství MeSH
- živiny * metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
The soil microbiota exhibits an important function in the ecosystem, and its response to climate change is of paramount importance for sustainable agroecosystems. The macronutrients, micronutrients, and additional constituents vital for the growth of plants are cycled biogeochemically under the regulation of the soil microbiome. Identifying and forecasting the effect of climate change on soil microbiomes and ecosystem services is the need of the hour to address one of the biggest global challenges of the present time. The impact of climate change on the structure and function of the soil microbiota is a major concern, explained by one or more sustainability factors around resilience, reluctance, and rework. However, the past research has revealed that microbial interventions have the potential to regenerate soils and improve crop resilience to climate change factors. The methods used therein include using soil microbes' innate capacity for carbon sequestration, rhizomediation, bio-fertilization, enzyme-mediated breakdown, phyto-stimulation, biocontrol of plant pathogens, antibiosis, inducing the antioxidative defense pathways, induced systemic resistance response (ISR), and releasing volatile organic compounds (VOCs) in the host plant. Microbial phytohormones have a major role in altering root shape in response to exposure to drought, salt, severe temperatures, and heavy metal toxicity and also have an impact on the metabolism of endogenous growth regulators in plant tissue. However, shelf life due to the short lifespan and storage time of microbial formulations is still a major challenge, and efforts should be made to evaluate their effectiveness in crop growth based on climate change. This review focuses on the influence of climate change on soil physico-chemical status, climate change adaptation by the soil microbiome, and its future implications.
Rare and unknown actinobacteria from unexplored environments have the potential to produce new bioactive molecules. This study aimed to use 16 s rRNA metabarcoding to determine the composition of the actinobacterial community, particularly focusing on rare and undescribed species, in a nature reserve within the Brazilian Cerrado called Sete Cidades National Park. Since this is an inaccessible area without due legal authorization, it is understudied, and, therefore, its diversity and biotechnological potential are not yet fully understood, and it may harbor species with groundbreaking genetic potential. In total, 543 operational taxonomic units (OTUs) across 14 phyla were detected, with Actinobacteria (41.2%), Proteobacteria (26.5%), and Acidobacteria (14.3%) being the most abundant. Within Actinobacteria, 107 OTUs were found, primarily from the families Mycobacteriaceae, Pseudonocardiaceae, and Streptomycetaceae. Mycobacterium and Streptomyces were the predominant genera across all samples. Seventeen rare OTUs with relative abundance < 0.1% were identified, with 82.3% found in only one sample yet 25.5% detected in all units. Notable rare and transient genera included Salinibacterium, Nocardia, Actinomycetospora_01, Saccharopolyspora, Sporichthya, and Nonomuraea. The high diversity and distribution of Actinobacteria OTUs indicate the area's potential for discovering new rare species. Intensified prospection on underexplored environments and characterization of their actinobacterial diversity could lead to the discovery of new species capable of generating innovative natural products.
- MeSH
- Actinobacteria * chemie klasifikace genetika izolace a purifikace MeSH
- biodiverzita MeSH
- metagenom MeSH
- půda chemie MeSH
- půdní mikrobiologie * MeSH
- RNA ribozomální 16S analýza MeSH
- taxonomické DNA čárové kódování MeSH
- veřejné parky MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Brazílie MeSH
The synchronous research and analysis of total and active soil microbial communities can provide insight into how these communities are impacted by continuous cropping years and pathogen infection. The diversity of total and active bacteria in rhizospheric soil of 2-year-old and 3-year-old healthy and diseased Panax notoginseng can comprehensively reveal the bacterial response characteristics in continuous cropping practice. The results showed that 4916 operational taxonomic units (OTUs) were found in the rhizospheric soil bacterial community of P. notoginseng at the DNA level, but only 2773 OTUs were found at the RNA level. The rhizospheric environment had significant effects on the active and bacterial communities, as indicated by the number of OTUs, Shannon, Chao1, Faith's phylogenetic diversity (Faith's PD), and Simpson's diversity indexes. The DNA level can better show the difference in diversity level before and after infection with root rot. The bacterial Chao1 and Faith's PD diversity indexes of 2-year-old root rot-diseased P. notoginseng rhizospheric soil (D2) were higher than that of healthy plants, while the bacterial Shannon diversity index of 3-year-old root rot-diseased P. notoginseng rhizospheric soil (D3) was the lowest in the total bacteria. Principal coordinate analysis (PCoA) illustrated that the total bacterial species composition changed markedly after root rot disease. There were significant differences in the composition of active bacterial species between the 2-year and 3-year rhizospheres. In conclusion, the total and active edaphic rhizospheric bacterial communities could provide important opportunities to understand the responses of bacteria to continuous cropping of P. notoginseng.
- MeSH
- Bacteria * klasifikace genetika izolace a purifikace MeSH
- biodiverzita * MeSH
- DNA bakterií genetika MeSH
- fylogeneze * MeSH
- kořeny rostlin mikrobiologie MeSH
- nemoci rostlin mikrobiologie MeSH
- Panax notoginseng * mikrobiologie MeSH
- půda chemie MeSH
- půdní mikrobiologie * MeSH
- rhizosféra * MeSH
- RNA ribozomální 16S genetika MeSH
- Publikační typ
- časopisecké články MeSH
Despite covering <5% of Earth's terrestrial area, peatlands are crucial for global carbon storage and are hot spots of methane cycling. This study examined the dynamics of aerobic and anaerobic methane oxidation in two undisturbed peatlands: a fen and a spruce swamp forest. Using microcosm incubations, we investigated the effect of ammonium addition, at a level similar to current N pollution processes, on aerobic methane oxidation. Our findings revealed higher methane consumption rates in fen compared to swamp peat, but no effect of ammonium amendment on methane consumption was found. Members of Methylocystis and Methylocella were the predominant methanotrophs in both peatlands. Furthermore, we explored the role of ferric iron and sulfate as electron acceptors for the anaerobic oxidation of methane (AOM). AOM occurred without the addition of an external electron acceptor in the fen, but not in the swamp peat. AOM was stimulated by sulfate and ferric iron addition in the swamp peat and inhibited by ferric iron in the fen. Our findings suggest that aerobic methane oxidizers are not N-limited in these peatlands and that there is an intrinsic potential for AOM in these environments, partially facilitated by ferric iron and sulfate acting as electron acceptors.
Secondary metabolites produced by myxobacterial genera are often characterized as diverse molecules with unique structural properties which drove us to search for myxobacterial source of anti-diabetic drug discovery. In the present study, from 80 soil samples, out of sixty-five observed isolates, 30 and 16 were purified as Myxococcus and non-Myxococcus, respectively. Isolated strains taxonomically belonged to the genera Myxococcus, Corallococcus and Cystobacter, Archangium, Nanocystis, and Sorangium, and some could not be attributed. Secondary metabolites of selected non-Myxococcus isolates extracted by the liquid-liquid method showed that the myxobacterium UTMC 4530 demonstrated the highest inhibition on the formation of carbonyl group and fructosamine, respectively. In addition, it showed 23% and 15.8% inhibitory activity on α-glucosides and α-amylase compared to acarbose (23%, 18%), respectively. The extract of strain UTMC 4530 showed 35% induction effect on glucose adsorption while showing no radical scavenging activity and no toxic effect on HRBC lysis and HepG2 in cytotoxicity assays. The strain UTMC 4530 (ON808962), with the multiple antidiabetic activity, showed 87.3% similarity to Corallococcus llansteffanensis which indicates its affiliation to a new genus. The results of this study revealed that secondary metabolites produced by strain UTMC 4530 can be considered a promising source to find new therapeutic and pharmaceutical applications perhaps a multi-mechanism anti-diabetic compound.
- MeSH
- fylogeneze MeSH
- Myxococcales * metabolismus MeSH
- Myxococcus * MeSH
- půda chemie MeSH
- půdní mikrobiologie MeSH
- Publikační typ
- časopisecké články MeSH
Phosphate-solubilising fungi (PSF) are beneficial microorganisms that play a pivotal role in plant growth by increasing the availability of phosphorus (P) in soil. Although phosphorus is an essential nutrient for plants, it often becomes inaccessible as it binds into insoluble forms. PSF effectively facilitate the release of this bound phosphorus through diverse mechanisms. Numerous fungal species demonstrate the ability to solubilise various types of phosphate compounds. Among the commonly researched PSF are Penicillium, Aspergillus, Rhizopus, Fusarium, Trichoderma, and Sclerotium. Moreover, yeasts such as Saccharomyces cerevisiae can potentially be leveraged as PSF. PSF secrete organic acids that chelate phosphate ions, thereby increasing their solubility in the soil. Moreover, PSF contribute to the decomposition of organic phosphorus compounds in soil by employing enzymes such as phosphatases, phytases, and phosphonatases. Furthermore, PSF can interact with other soil microorganisms, including nitrogen-fixing bacteria and arbuscular mycorrhizal fungi (AM-fungi), fostering synergistic effects that further enhance plant growth and nutrient absorption. The utilisation of PSF as biofertilisers offers numerous advantages over chemical fertilisers, including environmental friendliness, cost-effectiveness, and enhanced fertiliser utilisation efficiency. Furthermore, PSF can prove beneficial in challenging environments characterised by high phosphate sorption. Hence, this review serves as an updated study aimed at broadening the understanding of PSF and its potential applications in P solubilisation. This review also focuses on the diversity of PSF, the mechanisms underlying solubilisation, ecological roles of PSF in soil microbiome, and the benefits of sustainable agriculture. By delving into the ecological roles of PSF and their potential as biofertilisers, this study contributes to a deeper understanding of sustainable agriculture practices and addresses challenges in phosphate-scarce environments.
- MeSH
- fosfáty * metabolismus MeSH
- fosfor metabolismus MeSH
- houby * metabolismus růst a vývoj MeSH
- mykorhiza metabolismus fyziologie MeSH
- průmyslová hnojiva * analýza MeSH
- půda chemie MeSH
- půdní mikrobiologie * MeSH
- vývoj rostlin * MeSH
- zemědělství * metody MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
There is an increasing demand for bioinoculants based on plant growth-promoting rhizobacteria (PGPR) for use in agricultural ecosystems. However, there are still concerns and limited data on their reproducibility in different soil types and their effects on endemic rhizosphere communities. Therefore, this study explored the effects of inoculating the PGPR, Pseudomonas fluorescens strain UM270, on maize growth (Zea mays L.) and its associated rhizosphere bacteriome by sequencing the 16S ribosomal genes under greenhouse conditions. The results showed that inoculation with PGPR P. fluorescens UM270 improved shoot and root dry weights, chlorophyll concentration, and total biomass in the three soil types evaluated (clay, sandy-loam, and loam) compared to those of the controls. Bacterial community analysis of the three soil types revealed that maize plants inoculated with the UM270 strain showed a significant increase in Proteobacteria and Acidobacteria populations, whereas Actinobacteria and Bacteroidetes decreased. Shannon, Pielou, and Faith alpha-biodiversity indices did not reveal significant differences between treatments. Beta diversity revealed a bacterial community differential structure in each soil type, with some variation among treatments. Finally, some bacterial groups were found to co-occur and co-exclude with respect to UM270 inoculation. Considered together, these results show that PGPR P. fluorescens UM270 increases maize plant growth and has an important effect on the resident rhizobacterial communities of each soil type, making it a potential agricultural biofertilizer.
- MeSH
- Bacteria klasifikace genetika izolace a purifikace růst a vývoj MeSH
- biodiverzita MeSH
- biomasa MeSH
- fylogeneze MeSH
- kořeny rostlin * mikrobiologie růst a vývoj MeSH
- kukuřice setá * mikrobiologie růst a vývoj MeSH
- Pseudomonas fluorescens * genetika růst a vývoj fyziologie MeSH
- půda * chemie MeSH
- půdní mikrobiologie * MeSH
- rhizosféra * MeSH
- RNA ribozomální 16S genetika MeSH
- Publikační typ
- časopisecké články MeSH
The aim of the current study was to screen and identify heavy metal (chromium, cadmium, and lead) associated bacteria from petroleum-contaminated soil of district Muzaffarabad, Azad Jammu and Kashmir, Pakistan to develop ecofriendly technology for contaminated soil remediation. The petroleum-contaminated soil was collected from 99 different localities of district Muzaffarabad and the detection of heavy metals via an atomic absorption spectrometer. The isolation and identification of heavy metals-associated bacteria were done via traditional and molecular methods. Resistogram and antibiogram analysis were also performed using agar well diffusion and agar disc diffusion methods. The isolated bacteria were classified into species, i.e., B. paramycoides, B. albus, B. thuringiensis, B. velezensis, B. anthracis, B. pacificus Burkholderia arboris, Burkholderia reimsis, Burkholderia aenigmatica, and Streptococcus agalactiae. All heavy metals-associated bacteria showed resistance against both high and low concentrations of chromium while sensitive towards high and low concentrations of lead in the range of 3.0 ± 0.0 mm to 13.0 ± 0.0 mm and maximum inhibition was recorded when cadmium was used. Results revealed that some bacteria showed sensitivity towards Sulphonamides, Norfloxacin, Erythromycin, and Tobramycin. It was concluded that chromium-resistant bacteria could be used as a favorable source for chromium remediation from contaminated areas and could be used as a potential microbial filter.
- MeSH
- antibakteriální látky * farmakologie MeSH
- Bacteria * účinky léků klasifikace izolace a purifikace genetika MeSH
- chrom metabolismus MeSH
- kadmium analýza MeSH
- látky znečišťující půdu * analýza MeSH
- mikrobiální testy citlivosti * MeSH
- olovo MeSH
- půda chemie MeSH
- půdní mikrobiologie * MeSH
- ropa mikrobiologie analýza MeSH
- těžké kovy * farmakologie analýza MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Pákistán MeSH
Thallium (Tl) is a highly toxic trace metal, included in the US EPA list of priority pollutants. Even though its toxicity is potentially higher or comparable to Cd or Hg, its environmental impact is largely unknown. Despite its toxicity, only a few recent studies are mapping the impact of recently introduced Tl on soil microbial communities, namely in agricultural systems but no studies focus on its long term effect. To complement the understanding of the impact of Tl on soil, this study aims to describe the influence of extremely high naturally occurring Tl concentration (50 mg/kg of potentially bioavailable Tl) on soil microbial communities. Our investigation concentrated on samples collected at Buus (Erzmatt, Swiss Jura, Switzerland), encompassing forest and meadow soil profiles of the local soil formed on hydrothermally mineralized dolomite rock, which is naturally rich in Tl. The soil profiles showed a significant proportion of potentially bioavailable Tl. Yet, even this high concentration of Tl has a limited impact on the richness of the soil bacterial community. Only the meadow soil samples show a reduced richness compared to control samples. Furthermore, our analysis of geogenic Tl contamination in the region unveiled a surprising finding: compared to other soils of Switzerland and in stark contrast to soils affected by recent mining activities, the structure of the bacterial community in Buus remained relatively unaffected. This observation highlights the unique ability of soil microbial communities to withstand extreme Tl contamination. Our study advances the understanding of Tl's environmental impact and underscores the resilience of soil microbes in the face of severe long-term contamination.
