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Kifle BA, Sime AM, Gemeda MT, Woldesemayat AA. Shotgun metagenomic insights into secondary metabolite biosynthetic gene clusters reveal taxonomic and functional profiles of microbiomes in natural farmland soil. Sci Rep 2024; 14:15096. [PMID: 38956049 PMCID: PMC11220033 DOI: 10.1038/s41598-024-63254-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 05/27/2024] [Indexed: 07/04/2024] Open
Abstract
Antibiotic resistance is a worldwide problem that imposes a devastating effect on developing countries and requires immediate interventions. Initially, most of the antibiotic drugs were identified by culturing soil microbes. However, this method is prone to discovering the same antibiotics repeatedly. The present study employed a shotgun metagenomics approach to investigate the taxonomic diversity, functional potential, and biosynthetic capacity of microbiomes from two natural agricultural farmlands located in Bekeka and Welmera Choke Kebelle in Ethiopia for the first time. Analysis of the small subunit rRNA revealed bacterial domain accounting for 83.33% and 87.24% in the two selected natural farmlands. Additionally, the analysis showed the dominance of Proteobacteria representing 27.27% and 28.79% followed by Actinobacteria making up 12.73% and 13.64% of the phyla composition. Furthermore, the analysis revealed the presence of unassigned bacteria in the studied samples. The metagenome functional analysis showed 176,961 and 104, 636 number of protein-coding sequences (pCDS) from the two samples found a match with 172,655 and 102, 275 numbers of InterPro entries, respectively. The Genome ontology annotation suggests the presence of 5517 and 3293 pCDS assigned to the "biosynthesis process". Numerous Kyoto Encyclopedia of Genes and Genomes modules (KEGG modules) involved in the biosynthesis of terpenoids and polyketides were identified. Furthermore, both known and novel Biosynthetic gene clusters, responsible for the production of secondary metabolites, such as polyketide synthases, non-ribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptides (Ripp), and Terpene, were discovered. Generally, from the results it can be concluded that the microbiomes in the selected sampling sites have a hidden functional potential for the biosynthesis of secondary metabolites. Overall, this study can serve as a strong preliminary step in the long journey of bringing new antibiotics to the market.
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Affiliation(s)
- Bezayit Amare Kifle
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
| | - Amsale Melkamu Sime
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
| | - Mesfin Tafesse Gemeda
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
| | - Adugna Abdi Woldesemayat
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia.
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Vaish S, Soni SK, Singh B, Garg N, Zareen Ahmad I, Manoharan M, Trivedi AK. Meta-analysis of biodynamic (BD) preparations reveal the bacterial population involved in improving soil health, crop yield and quality. J Genet Eng Biotechnol 2024; 22:100345. [PMID: 38494258 PMCID: PMC10980875 DOI: 10.1016/j.jgeb.2023.100345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 12/23/2023] [Indexed: 03/19/2024]
Abstract
BACKGROUND Bacterial community found in biodynamic preparations (BD500-BD507) can help improve soil health, plant development, yield, and quality. The current work describes a metagenomic investigation of these preparations to identify the bacterial communities along with the functional diversity present within them. RESULTS Metagenome sequencing was performed using the Illumina MiSeq platform, which employs next-generation sequencing (NGS) technology, to provide an understanding of the bacterial communities and their functional diversity in BD preparations. NGS data of BD preparations revealed that maximum operational taxonomic units (OTUs) of the phylum Proteobacteria were present in BD506 (23429) followed by BD505 (22712) and BD501 (21591), respectively. Moreover, unclassified phylum (16657) and genus (16657) were also highest in BD506. Maximum alpha diversity was reported in BD501 (1095 OTU) and minimum in BD507 (257 OTU). Further, the OTUs for five major metabolic functional groups viz carbohydrate metabolism, xenobiotic degradation, membrane transport functions, energy metabolism, and enzyme activities were abundant in BD506 and BD501. CONCLUSION The bacterial communities in BD506 and BD501 are found to be unique and rare; they belong to functional categories that are involved in enzyme activity, membrane transport, xenobiotic degradation, and carbohydrate metabolism. These preparations might therefore be thought to be more effective. The investigation also found a highly varied population of bacteria, which could explain why BD preparations work well in the field. In view of this, the BD preparations may be utilized for unexploited bacterial communities for sustainable agriculture production.
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Affiliation(s)
- Supriya Vaish
- Division of Post Harvest Management, ICAR-Central Institute for Subtropical Horticulture, Rehmankhera, P.O. Kakori, Lucknow, Uttar Pradesh 226101, India
| | - Sumit K Soni
- Division of Crop Improvement and Biotechnology, ICAR-Central Institute for Subtropical Horticulture, Rehmankhera, P.O. Kakori, Lucknow, Uttar Pradesh 226101, India.
| | - Balvindra Singh
- Division of Post Harvest Management, ICAR-Central Institute for Subtropical Horticulture, Rehmankhera, P.O. Kakori, Lucknow, Uttar Pradesh 226101, India
| | - Neelima Garg
- Division of Post Harvest Management, ICAR-Central Institute for Subtropical Horticulture, Rehmankhera, P.O. Kakori, Lucknow, Uttar Pradesh 226101, India.
| | - Iffat Zareen Ahmad
- Department of Bioengineering, Integral University, Lucknow, Uttar Pradesh 226026, India
| | - Muthukumar Manoharan
- Division of Crop Improvement and Biotechnology, ICAR-Central Institute for Subtropical Horticulture, Rehmankhera, P.O. Kakori, Lucknow, Uttar Pradesh 226101, India
| | - Ajaya Kumar Trivedi
- Division of Post Harvest Management, ICAR-Central Institute for Subtropical Horticulture, Rehmankhera, P.O. Kakori, Lucknow, Uttar Pradesh 226101, India
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Fenibo EO, Nkuna R, Matambo T. Impact of artisanal refining activities on bacterial diversity in a Niger Delta fallow land. Sci Rep 2024; 14:3866. [PMID: 38365802 PMCID: PMC10873323 DOI: 10.1038/s41598-024-53147-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 01/29/2024] [Indexed: 02/18/2024] Open
Abstract
Hydrocarbon pollution is a major ecological problem facing oil-producing countries, especially in the Niger Delta region of Nigeria. In this study, a site that had been previously polluted by artisanal refining activity was investigated using 16S rRNA Illumina high-throughput sequencing technology and bioinformatics tools. These were used to investigate the bacterial diversity in soil with varying degrees of contamination, determined with a gas chromatography-flame ionization detector (GC-FID). Soil samples were collected from a heavily polluted (HP), mildly polluted (MP), and unpolluted (control sample, CS) portion of the study site. DNA was extracted using the Zymo Research (ZR) Fungi/Bacteria DNA MiniPrep kit, followed by PCR amplification and agarose gel electrophoresis. The microbiome was characterized based on the V3 and V4 hypervariable regions of the 16S rRNA gene. QIIME (Quantitative Insights Into Microbial Ecology) 2 software was used to analyse the sequence data. The final data set covered 20,640 demultiplexed high-quality reads and a total of 160 filtered bacterial OTUs. Proteobacteria dominated samples HP and CS, while Actinobacteria dominated sample MP. Denitratisoma, Pseudorhodoplanes, and Spirilospora were the leading genera in samples HP, CS, and MP respectively. Diversity analysis indicated that CS [with 25.98 ppm of total petroleum hydrocarbon (TPH)] is more diverse than HP (with 490,630 ppm of TPH) and MP (with 5398 ppm of TPH). A functional prediction study revealed that six functional modules dominated the dataset, with metabolism covering up to 70%, and 11 metabolic pathways. This study demonstrates that a higher hydrocarbon concentration in soil adversely impacts microbial diversity, creating a narrow bacterial diversity dominated by hydrocarbon-degrading species, in addition to the obvious land and ecosystem degradation caused by artisanal refining activities. Overall, the artisanal refining business is significantly driving ecosystem services losses in the Niger Delta, which calls for urgent intervention, with focus on bioremediation.
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Affiliation(s)
- Emmanuel Oliver Fenibo
- World Bank Africa Centre of Excellence for Oilfield Chemical Research, University of Port Harcourt, Choba, Rivers State, Nigeria.
| | - Rosina Nkuna
- Department of Biotechnology, Faculty of Applied and Computer Sciences, Vaal University of Technology, Vanderbijlpark 1900, Gauteng, South Africa
- Centre for Competence in Environmental Biotechnology, College of Animal and Environmental Science, University of South Africa, Florida Science Campus, Roodepoort, South Africa
| | - Tonderayi Matambo
- Centre for Competence in Environmental Biotechnology, College of Animal and Environmental Science, University of South Africa, Florida Science Campus, Roodepoort, South Africa
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Tauro TP, Nezomba H, Mtambanengwe F, Mapfumo P. Increasing phosphorus rate alters microbial dynamics and soil available P in a Lixisol of Zimbabwe. PLoS One 2023; 18:e0291226. [PMID: 37682930 PMCID: PMC10490935 DOI: 10.1371/journal.pone.0291226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
Soil phosphorus (P) deficiency is a major challenge to food security in most parts of sub-Saharan Africa, including Zimbabwe, where farmers largely depend on local organic nutrient resources as fertilizer in the production of crops. Soil microorganisms can contribute to synchronous availability of soil P to plants through regulating immobilization and mineralization cycles of soil P pools but their activity may be influenced by antecedent soil P, P fertilizer application regimes and P uptake by plants. Using soils collected from plots where Crotalaria juncea (high quality), Calliandra calothyrsus (medium quality), cattle manure (variable quality), maize stover and Pinus patula sawdust (both low quality) were applied at the rate of 4 t C ha-1 with 16 kg P ha-1 at the start of every season over 16 seasons. A pot study was conducted to evaluate the influence of increasing inorganic P fertilizer rates (26 and 36 kg P ha-1) on soil microbial dynamics, soil P pools, and maize P uptake. Results indicated that nineteen (19) fungal and forty-two (42) bacterial colonies were identified over the study period. Fungi dominated bacteria on day one, with Aspergillus niger showing a 30-98% abundance that depends on organic resource quality. Overall, microbial diversity peaked activity characterized succession on day 29, which coincided with a significant (P<0.05) increase in P availability. Increasing P rate to 26 kg P ha-1 amplified the microbial diverse peak activity under medium-high quality resources while under the control the peak emerged earlier on day 15. Mucor and Bacillus had peak abundances on day 43 and 57, respectively, across treatments regardless of P rates. Treatment and P rate had a significant (P<0.01) effect on microbial P. Bacteria were more responsive to added P than fungi. Increasing P to 36 kg P ha-1 also stimulated an earlier microbial diverse peak activity under maize stover on day 15. Addition of P alone, without supplying complementary nutrients such as N, did not have a positive effect on maize P uptake. Farmers need to co-apply medium-high quality organic resources with high fertilizer P rates to increase microbial diversity, plant available P and maize growth on sandy soils (Lixisols). Our results suggest that there is a need to reconsider existing P fertilizer recommendations, currently pegged at between 26 and 30 kg P ha-1, for maize production on sandy soils as well as develop new fertilizer formulations to intensify crop production in Zimbabwe.
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Affiliation(s)
- Tonny P. Tauro
- Department of Soil Science & Environment, University of Zimbabwe, Harare, Zimbabwe
- Department of Natural Resources Management, Marondera University of Agricultural Sciences & Technology, Marondera, Zimbabwe
| | - Hatirarami Nezomba
- Department of Soil Science & Environment, University of Zimbabwe, Harare, Zimbabwe
| | | | - Paul Mapfumo
- Department of Soil Science & Environment, University of Zimbabwe, Harare, Zimbabwe
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Kuo J, Liu D, Lin CH. Functional Prediction of Microbial Communities in Sediment Microbial Fuel Cells. Bioengineering (Basel) 2023; 10:bioengineering10020199. [PMID: 36829693 PMCID: PMC9951962 DOI: 10.3390/bioengineering10020199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/25/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Sediment microbial fuel cells (MFCs) were developed in which the complex substrates present in the sediment could be oxidized by microbes for electron production. In this study, the functional prediction of microbial communities of anode-associated soils in sediment MFCs was investigated based on 16S rRNA genes. Four computational approaches, including BugBase, Functional Annotation of Prokaryotic Taxa (FAPROTAX), the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2), and Tax4Fun2, were applied. A total of 67, 9, 37, and 38 functional features were statistically significant. Among these functional groups, the function related to the generation of precursor metabolites and energy was the only one included in all four computational methods, and the sum total of the proportion was 93.54%. The metabolism of cofactor, carrier, and vitamin biosynthesis was included in the three methods, and the sum total of the proportion was 29.94%. The results suggested that the microbial communities usually contribute to energy metabolism, or the metabolism of cofactor, carrier, and vitamin biosynthesis might reveal the functional status in the anode of sediment MFCs.
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Affiliation(s)
- Jimmy Kuo
- Department of Planning and Research, National Museum of Marine Biology and Aquarium, Pingtung 94450, Taiwan
- Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung 94450, Taiwan
| | - Daniel Liu
- Department of Biomedical Sciences, Da-Yeh University, 168 University Road, Dacun, Changhua 51591, Taiwan
| | - Chorng-Horng Lin
- Department of Biomedical Sciences, Da-Yeh University, 168 University Road, Dacun, Changhua 51591, Taiwan
- Correspondence: ; Tel.: +886-4-8511888
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Guts Bacterial Communities of Porcellio dilatatus: Symbionts Predominance, Functional Significance and Putative Biotechnological Potential. Microorganisms 2022; 10:microorganisms10112230. [PMID: 36422301 PMCID: PMC9692603 DOI: 10.3390/microorganisms10112230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Terrestrial isopods are effective herbivorous scavengers with an important ecological role in organic matter cycling. Their guts are considered to be a natural enrichment environment for lignocellulosic biomass (LCB)-degrading bacteria. The main goal of this work was to assess the structural diversity of Porcellio dilatatus gut bacterial communities using NGS technologies, and to predict their functional potential using PICRUSt2 software. Pseudomonadota, Actinomycetota, Bacillota, Cyanobacteria, Mycoplasmatota, Bacteroidota, Candidatus Patescibacteria and Chloroflexota were the most abundant phyla found in P. dilatatus gut bacterial communities. At a family level, we identified the presence of eleven common bacterial families. Functionally, the P. dilatatus gut bacterial communities exhibited enrichment in KEGG pathways related to the functional module of metabolism. With the predicted functional profile of P. dilatatus metagenomes, it was possible to envision putative symbiotic relationships between P. dilatatus gut bacterial communities and their hosts. It was also possible to foresee the presence of a well-adapted bacterial community responsible for nutrient uptake for the host and for maintaining host homeostasis. Genes encoding LCB-degrading enzymes were also predicted in all samples. Therefore, the P. dilatatus digestive tract may be considered a potential source of LCB-degrading enzymes that is not to be neglected.
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7
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Gou Z, Liu G, Wang Y, Li X, Wang H, Chen S, Su Y, Sun Y, Ma NL, Chen G. Enhancing N uptake and reducing N pollution via green, sustainable N fixation-release model. ENVIRONMENTAL RESEARCH 2022; 214:113934. [PMID: 36027962 DOI: 10.1016/j.envres.2022.113934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/14/2022] [Accepted: 07/17/2022] [Indexed: 06/15/2023]
Abstract
The overuse of N fertilizers has caused serious environmental problems (e.g., soil acidification, excessive N2O in the air, and groundwater contamination) and poses a serious threat to human health. Improving N fertilizer utilization efficiency and plant uptake is an alternative for N fertilizers overuses. Enterobacter cloacae is an opportunistic pathogen, also used as plant growth-promoting rhizobacteria (PGPR), has been widely presented in the fields of bioremediation and bioprotection. Here we developed a new N fixation-release model by combining biochar with E. cloacae. The efficiency of the model was evaluated using a greenhouse pot experiment with maize (Zea mays L.) as the test crop. The results showed that biochar combined with E. cloacae significantly increased the N content. The application of biochar combined with E. cloacae increased total N in soil by 33% compared with that of N fertilizers application. The N-uptake and utilization efficiency (NUE) in plant was increased 17.03% and 14.18%, respectively. The activities of urease, dehydrogenase and fluorescein diacetate hydrolase (FDA) was improved, the catalase (CAT) activity decreased. Analysis of the microbial community diversity revealed the abundance of Proteobacteria, Actinobacteria, Firmicutes, and Gemmatimonadetes were significantly improved. The mechanism under the model is that E. cloacae acted as N-fixation by capturing N2 from air. Biochar served as carrier, supporting better living environment for E. cloacae, also as adsorbent adsorbing N from fertilizer and from fixed N by E. cloacae, the adsorption in turn slower the N release. Altogether, the model promotes N utilization by plants, improves the soil environment, and reduces N pollution.
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Affiliation(s)
- Zechang Gou
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Guoqing Liu
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Yisheng Wang
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Xiufeng Li
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Huiqiong Wang
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Siji Chen
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Yingjie Su
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Yang Sun
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China.
| | - Nyuk Ling Ma
- Faculty of Science and Marine Environment, University Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
| | - Guang Chen
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China.
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Liu Y, Xu Y, Cui X, Zhang B, Wang X, Qin X, Wang J, Li Y, Zhang W, Liu G, Chen T, Zhang G. Temporary Survival Increasing the Diversity of Culturable Heterotrophic Bacteria in the Newly Exposed Moraine at a Glacier Snout. BIOLOGY 2022; 11:biology11111555. [PMID: 36358257 PMCID: PMC9687651 DOI: 10.3390/biology11111555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/11/2022] [Accepted: 10/20/2022] [Indexed: 11/05/2022]
Abstract
Laohugou Glacier No. 12 is located on the northern slope of the western Qilian Mountains with a temperate continental wet climate and an extremely cold winter. Bacteria in a newly exposed moraine have to cope with various pressures owing to deglaciation at the glacier snout. However, limited information is available regarding the high diversity and temporary survival of culturable heterotrophic bacteria under various environmental stresses. To examine the tolerance of extremophiles against varying environmental conditions in a newly exposed moraine, we simulated environmental stress in bacterial cultures. The results showed that the isolated strains belonged to actinobacteria, Proteobacteria, Bacteroidetes, Deinococcus-Thermus, and Firmicutes. Actinobacteria was the most abundant phylum, followed by Proteobacteria, at both high and low temperatures. Pseudarthrobacter was the most abundant genus, accounting for 14.2% of the total isolates. Although several microorganisms grew at 10 °C, the proportion of microorganisms that grew at 25 °C was substantially higher. In particular, 50% of all bacterial isolates grew only at a high temperature (HT), whereas 21.4% of the isolates grew at a low temperature (LT), and 38.6% of the isolates grew at both HT and LT. In addition, many radiation-resistant extremophiles were identified, which adapted to both cold and oxidative conditions. The nearest neighbors of approximately >90% of bacteria belonged to a nonglacial environment, such as oil-contaminated soil, rocks, and black sand, instead of glacial niches. This study provides insights into the ecological traits, stress responses, and temporary survival of culturable heterotrophic bacteria in a newly exposed moraine with variable environmental conditions and the relationship of these communities with the non-glacial environment. This study may help to understand the evolution, competition, and selective growth of bacteria in the transition regions between glaciers and retreats in the context of glacier melting and retreat owing to global warming.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Yeteng Xu
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Xiaowen Cui
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- College of Geography and Environment Science, Northwest Normal University, Lanzhou 730070, China
| | - Binglin Zhang
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Xinyue Wang
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Xiang Qin
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Jinxiu Wang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Yanzhao Li
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- School of Stomatology, Lanzhou University, Lanzhou 730000, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Correspondence: (T.C.); (G.Z.)
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Correspondence: (T.C.); (G.Z.)
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Sood U, Dhingra GG, Anand S, Hira P, Kumar R, Kaur J, Verma M, Singhvi N, Lal S, Rawat CD, Singh VK, Kaur J, Verma H, Tripathi C, Singh P, Dua A, Saxena A, Phartyal R, Jayaraj P, Makhija S, Gupta R, Sahni S, Nayyar N, Abraham JS, Somasundaram S, Lata P, Solanki R, Mahato NK, Prakash O, Bala K, Kumari R, Toteja R, Kalia VC, Lal R. Microbial Journey: Mount Everest to Mars. Indian J Microbiol 2022; 62:323-337. [PMID: 35974919 PMCID: PMC9375815 DOI: 10.1007/s12088-022-01029-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/01/2022] [Indexed: 11/05/2022] Open
Abstract
A rigorous exploration of microbial diversity has revealed its presence on Earth, deep oceans, and vast space. The presence of microbial life in diverse environmental conditions, ranging from moderate to extreme temperature, pH, salinity, oxygen, radiations, and altitudes, has provided the necessary impetus to search for them by extending the limits of their habitats. Microbiology started as a distinct science in the mid-nineteenth century and has provided inputs for the betterment of mankind during the last 150 years. As beneficial microbes are assets and pathogens are detrimental, studying both have its own merits. Scientists are nowadays working on illustrating the microbial dynamics in Earth's subsurface, deep sea, and polar regions. In addition to studying the role of microbes in the environment, the microbe-host interactions in humans, animals and plants are also unearthing newer insights that can help us to improve the health of the host by modulating the microbiota. Microbes have the potential to remediate persistent organic pollutants. Antimicrobial resistance which is a serious concern can also be tackled only after monitoring the spread of resistant microbes using disciplines of genomics and metagenomics The cognizance of microbiology has reached the top of the world. Space Missions are now looking for signs of life on the planets (specifically Mars), the Moon and beyond them. Among the most potent pieces of evidence to support the existence of life is to look for microbial, plant, and animal fossils. There is also an urgent need to deliberate and communicate these findings to layman and policymakers that would help them to take an adequate decision for better health and the environment around us. Here, we present a glimpse of recent advancements by scientists from around the world, exploring and exploiting microbial diversity.
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Affiliation(s)
- Utkarsh Sood
- The Energy and Resources Institute, New Delhi, India
| | | | - Shailly Anand
- Deen Dayal Upadhyaya College, University of Delhi, New Delhi, India
| | - Princy Hira
- Maitreyi College, University of Delhi, New Delhi, India
| | - Roshan Kumar
- Post-Graduate Department of Zoology, Magadh University, Bodh Gaya, Bihar India
| | | | - Mansi Verma
- Sri Venkateswara College, University of Delhi, New Delhi, India
| | | | - Sukanya Lal
- Ramjas College, University of Delhi, Delhi, India
| | | | | | - Jaspreet Kaur
- Maitreyi College, University of Delhi, New Delhi, India
| | | | | | - Priya Singh
- Maitreyi College, University of Delhi, New Delhi, India
| | - Ankita Dua
- Shivaji College, University of Delhi, New Delhi, India
| | - Anjali Saxena
- Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi, India
| | | | - Perumal Jayaraj
- Sri Venkateswara College, University of Delhi, New Delhi, India
| | - Seema Makhija
- Acharya Narendra Dev College, University of Delhi, Delhi, India
| | - Renu Gupta
- Maitreyi College, University of Delhi, New Delhi, India
| | - Sumit Sahni
- Acharya Narendra Dev College, University of Delhi, Delhi, India
| | - Namita Nayyar
- Sri Venkateswara College, University of Delhi, New Delhi, India
| | | | | | - Pushp Lata
- Ramjas College, University of Delhi, Delhi, India
| | - Renu Solanki
- Deen Dayal Upadhyaya College, University of Delhi, New Delhi, India
| | - Nitish Kumar Mahato
- University Department of Zoology, Kolhan University, Chaibasa, Jharkhand India
| | - Om Prakash
- National Centre for Cell Sciences, Pune, Maharashtra India
| | - Kiran Bala
- Deshbandhu College, University of Delhi, New Delhi, India
| | - Rashmi Kumari
- College of Commerce, Arts and Science, Patliputra University, Patna, Bihar India
| | - Ravi Toteja
- Acharya Narendra Dev College, University of Delhi, Delhi, India
| | | | - Rup Lal
- The Energy and Resources Institute, New Delhi, India
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10
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de Souza AJ, de Araújo Pereira AP, Pedrinho A, Andreote FD, Tornisielo VL, Tizioto PC, Coutinho LL, Regitano JB. Land use and roles of soil bacterial community in the dissipation of atrazine. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 827:154239. [PMID: 35245545 DOI: 10.1016/j.scitotenv.2022.154239] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 06/14/2023]
Abstract
Atrazine (ATZ) is one of the most widely used herbicides in the world even though it is classified as a carcinogenic endocrine disruptor. This study focused on how land use (grazing versus cultivation in parallel soils, the latter under no-till with a seven-year history of ATZ application) and bacterial community diversity affected ATZ dissipation. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Acidobacteria, Verrucomicrobia, Planctomycetes, and Gemmatimonadetes were the dominant phyla in both soils. The mineralization of ATZ was much higher in soils under cultivation up to the onset of moderate diversity depletion (dilution =10-3), corresponding to 44-52% of the amount applied (< 5% in the grazed soil). This was attributed to the higher diversity and complexity of the soils´ bacterial communities which consist of microbial groups that were more adapted as a result of previous exposure to ATZ. In these cases, ATZ dissipation was attributed mainly to mineralization (DT50 = 4-11 d). However, formation of non-extractable ATZ residues was exceptionally important in the other cases (DT50 = 17-44 d). The cultivated soils also presented a higher number of bacterial genera correlated with ATZ dissipation, in which Acidothermus, Aquicela, Arenimonas, Candidatus_Koribacter, Hirschia, MND1, Nitrospira, Occallatibacter, OM27_clade, and Ralstonia are suggested as potential ATZ-degraders. Finally, ATZ dissipation was mostly associated with an abundance of microbial functions related to energy supply and N-metabolism, suggesting co-metabolism is its first biodegradation step.
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Affiliation(s)
- Adijailton Jose de Souza
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Alexandre Pedrinho
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Fernando Dini Andreote
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Valdemar Luiz Tornisielo
- Center of Nuclear Energy for Agriculture (CENA), University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Luiz Lehmann Coutinho
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Jussara Borges Regitano
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil.
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11
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Shifts in Bacterial Community Composition and Functional Traits at Different Time Periods Post-deglaciation of Gangotri Glacier, Himalaya. Curr Microbiol 2022; 79:91. [PMID: 35129698 DOI: 10.1007/s00284-022-02779-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/20/2022] [Indexed: 11/03/2022]
Abstract
Climate change causes an unprecedented increase in glacial retreats. The melting ice exposes land for colonization and diversification of bacterial communities leading to soil development, changes in plant community composition, and ecosystem functioning. Although a few studies have focused on macro-level deglaciation impacts, little is known about such effects on the bacterial community succession. Here, we provide meta-barcoding-based insight into the ecological attributes of bacterial community across different retreating periods of the Gangotri glacier, western Himalaya. We selected three sites along a terminal moraine representing recent (~ 20 yrs), intermediate (~ 100 yrs), and late (~ 300 yrs) deglaciation periods. Results showed that the genus Mycobacterium belonging to phylum Actinobacteria dominated recently deglaciated land. Relative abundance of these pioneer bacterial taxa decreased by 20-50% in the later stages with the emergence of new and rising of the less abundant members of the phyla Proteobacteria, Firmicutes, Planctomycetes, Acidobacteria, Verrucomicrobia, Candidatus TM6, and Chloroflexi. The community in the recent stage was less rich and harbored competitive interactions, while the later stages experienced a surge in bacterial diversity with cooperative interactions. The shift in α-diversity and composition was strongly influenced by soil organic carbon, carbon to nitrogen ratio, and soil moisture content. The functional analyses revealed a progression from a metabolism focused to a functionally progressive community required for bacterial co-existence and succession in plant communities. Overall, the findings indicate that the bacterial communities inhabit, diversify, and develop specialized functions post-deglaciation leading to nutrient inputs to soil and vegetation development, which may provide feedback to climate change.
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12
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Mafiz AI, He Y, Zhang W, Zhang Y. Soil Bacteria in Urban Community Gardens Have the Potential to Disseminate Antimicrobial Resistance Through Horizontal Gene Transfer. Front Microbiol 2021; 12:771707. [PMID: 34887843 PMCID: PMC8650581 DOI: 10.3389/fmicb.2021.771707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/14/2021] [Indexed: 11/29/2022] Open
Abstract
Fifteen soil and 45 vegetable samples from Detroit community gardens were analyzed for potential antimicrobial resistance contamination. Soil bacteria were isolated and tested by antimicrobial susceptibility profiling, horizontal gene transfer, and whole-genome sequencing. High-throughput 16S rRNA sequencing analysis was conducted on collected soil samples to determine the total bacterial composition. Of 226 bacterial isolates recovered, 54 were from soil and 172 from vegetables. A high minimal inhibitory concentration (MIC) was defined as the MIC greater than or equal to the resistance breakpoint of Escherichia coli for Gram-negative bacteria or Staphylococcus aureus for Gram-positive bacteria. The high MIC was observed in 63.4 and 69.8% of Gram-negative isolates from soil and vegetables, respectively, against amoxicillin/clavulanic acid, as well as 97.5 and 82.7% against ampicillin, 97.6 and 90.7% against ceftriaxone, 85.4 and 81.3% against cefoxitin, 65.8 and 70.5% against chloramphenicol, and 80.5 and 59.7% against ciprofloxacin. All Gram-positive bacteria showed a high MIC to gentamicin, kanamycin, and penicillin. Forty of 57 isolates carrying tetM (70.2%) successfully transferred tetracycline resistance to a susceptible recipient via conjugation. Whole-genome sequencing analysis identified a wide array of antimicrobial resistance genes (ARGs), including those encoding AdeIJK, Mex, and SmeDEF efflux pumps, suggesting a high potential of the isolates to become antimicrobial resistant, despite some inconsistency between the gene profile and the resistance phenotype. In conclusion, soil bacteria in urban community gardens can serve as a reservoir of antimicrobial resistance with the potential to transfer to clinically important pathogens, resulting in food safety and public health concerns.
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Affiliation(s)
- Abdullah Ibn Mafiz
- Department of Nutrition and Food Science, Wayne State University, Detroit, MI, United States.,Department of Human Sciences, Tennessee State University, Nashville, TN, United States
| | - Yingshu He
- Department of Food Science and Nutrition, Illinois Institute of Technology, Chicago, IL, United States.,Center for Food Safety, University of Georgia, Griffin, GA, United States
| | - Wei Zhang
- Department of Food Science and Nutrition, Illinois Institute of Technology, Chicago, IL, United States
| | - Yifan Zhang
- Department of Nutrition and Food Science, Wayne State University, Detroit, MI, United States
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13
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Adeleke BS, Ayangbenro AS, Babalola OO. Bacterial community structure of the sunflower ( Helianthus annuus) endosphere. PLANT SIGNALING & BEHAVIOR 2021; 16:1974217. [PMID: 34590546 PMCID: PMC9208795 DOI: 10.1080/15592324.2021.1974217] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Agrochemical applications on farmland aim to enhance crop yield; however, the consequence of biodiversity loss has caused a reduction in ecological functions. The positive endosphere interactions and crop rotation systems may function in restoring a stable ecosystem. Employing culture-independent techniques will help access the total bacteria community in the sunflower endosphere. Limited information is available on the bacteria diversity in sunflower plants cultivated under different agricultural practices. Hence, this study was designed to investigate the endophytic bacterial community structure of sunflower at the growing stage. Plant root and stem samples were sourced from two locations (Itsoseng and Lichtenburg), for DNA extraction and sequenced on the Illumina Miseq platform. The sequence dataset was analyzed using online bioinformatics tools. Saccharibacteria and Acidobacteria were dominant in plant roots, while the stem is dominated by Proteobacteria, Bacteriodetes, and Gemmatimonadetes across the sites. Bacterial genera, Acidovorax, Flavobacterium, Hydrogenophaga, and Burkholderia-Paraburkhoderia were found dominant in the root, while the stem is dominated by Streptomyces. The diverse bacterial community structure at phyla and class levels were significantly different in plant organs across the sites. The influence of soil physical and chemical parameters analyzed was observed to induce bacterial distribution across the sites. This study provides information on the dominant bacteria community structure in sunflowers at the growing stage and their predictive functions, which suggest their future exploration as bioinoculants for improved agricultural yields.
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Affiliation(s)
- Bartholomew Saanu Adeleke
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Ayansina Segun Ayangbenro
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
- CONTACT Olubukola Oluranti Babalola Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho2735, South Africa
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14
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Stone W, Lukashe NS, Blake LI, Gwandu T, Hardie AG, Quinton J, Johnson K, Clarke CE. The microbiology of rebuilding soils with water treatment residual co-amendments: Risks and benefits. JOURNAL OF ENVIRONMENTAL QUALITY 2021; 50:1381-1394. [PMID: 34464455 DOI: 10.1002/jeq2.20286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
Water treatment residual (WTR) is composed of sludges from the potable water treatment process, currently largely destined for landfill. This waste can be diverted to rebuild degraded soils, aligning with the UN's Sustainable Development Goals 12 (Consumption and Production) and 15 (Terrestrial Ecosystems). Biosolids are tested against stringent pathogen guidelines, yet few studies have explored the microbial risk of WTR land application, despite anthropogenic impacts on water treatment. We explored the microbial risks and benefits of amending nutrient-poor sandy soil with WTRs. Our results showed that the culturable pathogen load of wet and dry WTRs did not warrant pre-processing before land application, according to South African national quality guidelines, with fecal coliforms not exceeding 104 colony forming units per gram dry weight in wet sludges sampled from four South African and Zimbabwean water treatment plants and decreasing upon drying and processing. There was no culturable pathogenic (fecal coliforms, enterococci, Salmonella, and Shigella) regrowth in soil incubations amended with dry WTR. However, the competition (microbial load and diversity) introduced by a WTR co-amendment did not limit pathogen survival in soils amended with biosolids. Application of WTR to nutrient-poor sandy soils for wheat (Triticum aestivum L.) growth improved the prokaryotic and eukaryotic culturable cell concentrations, similar to compost. However, the compost microbiome more significantly affected the bacterial beta diversity of the receiving soil than WTR when analyzed with automated ribosomal intergenic spacer analysis. Thus, although there was a low pathogen risk for WTR amendment in receiving soils and total soil microbial loads were increased, microbial diversity was more significantly enhanced by compost than WTR.
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Affiliation(s)
- Wendy Stone
- Environmental Microbiology Laboratory, Dep. of Microbiology, Stellenbosch Univ., Stellenbosch, 7602, South Africa
| | - Noxolo S Lukashe
- Dep. of Soil Science, Stellenbosch Univ., Stellenbosch, 7602, South Africa
| | | | - Tariro Gwandu
- Dep. of Engineering, Durham Univ., Durham, DH1 3LE, UK
- Dep. of Soil Science & Environment, Univ. of Zimbabwe, Harare, Zimbabwe
| | - Ailsa G Hardie
- Dep. of Soil Science, Stellenbosch Univ., Stellenbosch, 7602, South Africa
| | - John Quinton
- Lancaster Environment Centre, Lancaster Univ., Lancaster, Lancashire, UK
| | - Karen Johnson
- Dep. of Engineering, Durham Univ., Durham, DH1 3LE, UK
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15
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Tauro TP, Mtambanengwe F, Mpepereki S, Mapfumo P. Soil fungal community structure and seasonal diversity following application of organic amendments of different quality under maize cropping in Zimbabwe. PLoS One 2021; 16:e0258227. [PMID: 34648549 PMCID: PMC8516296 DOI: 10.1371/journal.pone.0258227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/21/2021] [Indexed: 11/18/2022] Open
Abstract
Recent advocacy for Integrated Soil Fertility Management (ISFM) in smallholder farming systems in east and southern Africa show substantial evidence of increased and sustained crop yields associated with enhanced soil productivity. However, the impact ISFM on soil fungi has received limited attention, yet fungi play key roles in crop growth. Following total soil DNA extraction with ZR soil microbe miniprep kit, illumina sequencing was used to, examine the fungal communities (ITS1F) under a maize crop following co-application of organic nutrient resources including Crotalaria juncea, cattle manure and maize stover with inorganic fertilizers at three-time periods (T1-December, T2-January, and T3-February) in Zimbabwe. Ninety-five fungal species were identified that were assigned to Ascomycota (>90%), Basidiomycota (7%) and Zygomycota (1%). At T1, Ascomycota and Basidiomycota were identified across treatments, with Ascomycota attaining > 93% frequency. Fungal succession was noted and involved reduction of Ascomycota coupled by increase in Basidiomycota under the different treatments. For example at T3, Basidiomycota increased to 34% while Ascomycota declined to 66% under manure but remained unchanged in other two organics. Pre-season mineral nitrogen (N) associated with the 'Birch effect' apparently influenced the fungal community structure at T1 while readily available fertilizer N was critical at T2 and T3. The low-quality maize stover promoted the presence of Exophiala sp SST 2011 and this was linked to N immobilization. The impact of N addition was more pronounced under medium (manure) to low-quality (maize stover) resources. Fungi required phosphorus (P) and N for survival while their proliferation was dependent on substrate availability linked to resource quality. Interactive-forward test indicated that soil available P and N were most influential (P < 0.05) factors shaping fungal communities. Co-application of medium to high quality organic and inorganic resources show promise as a sustainable entry point towards enhancing belowground fungal diversity critical in driving nutrient supply.
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Affiliation(s)
- Tonny P. Tauro
- Department of Soil Science & Environment, University of Zimbabwe, Mount Pleasant, Harare, Zimbabwe
- Department of Natural Resources Management, Marondera University of Agricultural Sciences & Technology, Marondera, Zimbabwe
| | - Florence Mtambanengwe
- Department of Soil Science & Environment, University of Zimbabwe, Mount Pleasant, Harare, Zimbabwe
| | - Shensi Mpepereki
- Department of Soil Science & Environment, University of Zimbabwe, Mount Pleasant, Harare, Zimbabwe
| | - Paul Mapfumo
- Department of Soil Science & Environment, University of Zimbabwe, Mount Pleasant, Harare, Zimbabwe
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16
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Prakash O, Parmar M, Vaijanapurkar M, Rale V, Shouche YS. Recent trend, biases and limitations of cultivation-based diversity studies of microbes. FEMS Microbiol Lett 2021; 368:6359716. [PMID: 34459476 DOI: 10.1093/femsle/fnab118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 08/27/2021] [Indexed: 12/22/2022] Open
Abstract
The current study attempts to analyze recent trends, biases and limitations of cultivation-based microbial diversity studies based on published, novel species in the past 6 years in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), an official publication of the International Committee on Systematics of Prokaryotes (ICSP) and the Bacteriology and Applied Microbiology (BAM) Division of the International Union of Microbiological Societies (IUMS). IJSEM deals with taxa that have validly published names under the International Code of Nomenclature of Prokaryotes (ICNP). All the relevant publications from the last 6 years were retrieved, sorted and analyzed to get the answers to What is the current rate of novel species description? Which country has contributed substantially and which phyla represented better in culturable diversity studies? What are the current limitations? Published data for the past 6 years indicate that 500-900 novel species are reported annually. China, Korea, Germany, UK, India and the USA are at the forefront while contributions from other nations are meager. Despite the recent development in culturomics tools the dominance of Proteobacteria, Bacteroidetes and Actinobacteria are still prevalent in cultivation, while the representation of archaea, obligate anaerobes, microaerophiles, synergistic symbionts, aerotolerant and other fastidious microbes is poor. Single strain-based taxonomic descriptions prevail and emphasis on objective-based cultivation for biotechnological and environmental significance is not yet conspicuous.
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Affiliation(s)
- Om Prakash
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune 411007, Maharashtra, India
| | - Mrinalini Parmar
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune 411007, Maharashtra, India
| | - Manali Vaijanapurkar
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune 411007, Maharashtra, India.,Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune-412115, Maharashtra, India
| | - Vinay Rale
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune-412115, Maharashtra, India
| | - Yogesh S Shouche
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune 411007, Maharashtra, India
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17
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Rathore P, Joy SS, Yadav R, Ramakrishna W. Co-occurrence and patterns of phosphate solubilizing, salt and metal tolerant and antibiotic-resistant bacteria in diverse soils. 3 Biotech 2021; 11:356. [PMID: 34249597 DOI: 10.1007/s13205-021-02904-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 06/19/2021] [Indexed: 11/28/2022] Open
Abstract
Soil is a treasure chest for beneficial bacteria with applications in diverse fields, which include agriculture, rhizoremediation, and medicine. Metagenomic analysis of four soil samples identified Proteobacteria as the dominant phylum (32-52%) followed by the phylum Acidobacteria (11-21% in three out of four soils). Bacteria that were prevalent at the highest level belong to the genus Kaistobacter (8-19%). PICRUSt analysis predicted KEGG functional pathways associated with the metagenomes of the four soils. The identified pathways could be attributed to metal tolerance, antibiotic resistance and plant growth promotion. The prevalence of phosphate solubilizing bacteria (PSB) was investigated in four soil samples, ranging from 26 to 59% of the total culturable bacteria. The abundance of salt-tolerant and metal-tolerant bacteria showed considerable variation ranging from 1 to 62% and 4-69%, respectively. In comparison, the soil with the maximum prevalence of temperature-tolerant and antibiotic-resistant bacteria was close 30%. In this study, the common pattern observed was that PSB were the most abundant in all types of soils compared to other traits. Conversely, most of the isolates, which are salt-tolerant, copper-tolerant, and ampicillin-resistant, showed phosphate solubilization activity. The sequencing of the partial 16S-rRNA gene revealed that PSB belonged to Bacillus genera. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02904-7.
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Affiliation(s)
- Parikshita Rathore
- Department of Biochemistry, Central University of Punjab, Bathinda, Punjab India
| | - Sherina Sara Joy
- Department of Biochemistry, Central University of Punjab, Bathinda, Punjab India
| | - Radheshyam Yadav
- Department of Biochemistry, Central University of Punjab, Bathinda, Punjab India
| | - Wusirika Ramakrishna
- Department of Biochemistry, Central University of Punjab, Bathinda, Punjab India
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18
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Microbial Diversity of Temperate Pine and Native Forest Soils Profiled by 16S rRNA Gene Amplicon Sequencing. Microbiol Resour Announc 2021; 10:10/20/e00298-21. [PMID: 34016677 PMCID: PMC8188351 DOI: 10.1128/mra.00298-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Most biodiversity measures indicate an ongoing deterioration due to intensifying anthropogenic pressures even though efforts are being intensified worldwide to conserve biodiversity. Knowledge of the implication of land-use change on soil bacterial communities is essential for ecosystem restoration. Most biodiversity measures indicate an ongoing deterioration due to intensifying anthropogenic pressures even though efforts are being intensified worldwide to conserve biodiversity. Knowledge of the implication of land use change on soil bacterial communities is essential for ecosystem restoration. Here, the effect of the conversion of native forests to temperate pine forests on soil bacterial diversity and community composition was investigated. The diversity and composition of the bacterial communities were affected by land use change across the sites.
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19
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Structural and Functional Shift in Soil Bacterial Community in Response to Long-Term Compost Amendment in Paddy Field. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11052183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Microbial community composition and diversity of agricultural soils primarily depend on management practices. The application of compost on agricultural fields is known to increase soil fertility, which can also help to enhance agricultural productivity. The effects of long-term application of compost along with nitrogen (N), phosphorus (P), and potassium (K) (+Compost) on soil bacterial diversity and community profiles were assessed by amplicon sequencing targeting the 16S rRNA gene of bacteria and compared with those on soils that received only NPK but not compost (−Compost). Ordination plot showed treatments to cluster differently, implying changes in community composition, which were validated with taxonomical data showing Firmicutes, Actinobacteria, and their related classes to be significantly higher in +Compost than in −Compost soils. The predicted abundance of functional genes related to plant growth promotion, development, and decomposition was significantly higher in compost-amended soil than in soils without compost. The results are of particular importance as they provide insights into designing management practices to promote agricultural sustainability.
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20
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Pacwa-Płociniczak M, Biniecka P, Bondarczuk K, Piotrowska-Seget Z. Metagenomic Functional Profiling Reveals Differences in Bacterial Composition and Function During Bioaugmentation of Aged Petroleum-Contaminated Soil. Front Microbiol 2020; 11:2106. [PMID: 32983067 PMCID: PMC7487420 DOI: 10.3389/fmicb.2020.02106] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/10/2020] [Indexed: 02/01/2023] Open
Abstract
Our objective was to study the bacterial community changes that determine enhanced removal of petroleum hydrocarbons from soils subjected to bioaugmentation with the hydrocarbon-degrading strains Rhodococcus erythropolis CD 130, CD 167, and their combination. To achieve this, a high-throughput sequencing of the 16S rRNA gene was performed. The changes in the bacterial community composition were most apparent the day after bacterial inoculation. These changes represented an increase in the percentage abundance of Rhodococcus and Pseudomonas genera. Surprisingly, members of the Rhodococcus genus were not present after day 91. At the end of the experiment, the bacterial communities from the CD 130, CD 167, and control soils had a similar structure. Nevertheless, the composition of the bacteria in the CD 130 + CD 167 soil was still distinct from the control. Metagenomic predictions from the 16S rRNA gene sequences showed that the introduction of bacteria had a significant influence on the predicted pathways (metabolism of xenobiotics, lipids, terpenoids, polyketides, and amino acids) on day one. On day 182, differences in the abundance of functional pathways were also detected in the CD 130 and CD 130 + CD 167 soils. Additionally, we observed that on day one, in all bioaugmented soils, the alkH gene was mainly contributed by the Rhodococcus and Mycobacterium genera, whereas in non-treated soil, this gene was contributed only by the Mycobacterium genus. Interestingly, from day 91, the Mycobacterium genus was the main contributor for the tested genes in all studied soils. Our results showed that hydrocarbon depletion from the analyzed soils resulted from the activity of the autochthonous bacteria. However, these changes in the composition and function of the indigenous bacterial community occurred under the influence of the introduced bacteria.
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Affiliation(s)
- Magdalena Pacwa-Płociniczak
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Paulina Biniecka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Kinga Bondarczuk
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Białystok, Poland
| | - Zofia Piotrowska-Seget
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
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21
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Lamelas A, Desgarennes D, López-Lima D, Villain L, Alonso-Sánchez A, Artacho A, Latorre A, Moya A, Carrión G. The Bacterial Microbiome of Meloidogyne-Based Disease Complex in Coffee and Tomato. FRONTIERS IN PLANT SCIENCE 2020; 11:136. [PMID: 32174936 PMCID: PMC7056832 DOI: 10.3389/fpls.2020.00136] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/29/2020] [Indexed: 02/05/2023]
Abstract
The Meloidogyne-based disease complexes (MDCs) are caused by the interaction of different root-knot nematode species and phytopathogenic fungi. These complexes are devastating several important crops worldwide including tomato and coffee. Despite their relevance, little is known about the role of the bacterial communities in the MDCs. In this study 16s rDNA gene sequencing was used to analyze the bacterial microbiome associated with healthy and infested roots, as well with females and eggs of Meloidogyne enterolobii and M. paranaensis, the causal agents of MDC in tomato and coffee, respectively. Each MDC pathosystems displayed a specific taxonomic diversity and relative abundances constituting a very complex system. The main bacterial drivers of the MDC infection process were identified for both crops at order level. While corky-root coffee samples presented an enrichment of Bacillales and Burkholderiales, the corcky-root tomato samples presented an enrichment on Saprospirales, Chthoniobacterales, Alteromonadales, and Xanthomonadales. At genus level, Nocardia was common to both systems, and it could be related to the development of tumor symptoms by altering both nematode and plant systems. Furthermore, we predicted the healthy metabolic profile of the roots microbiome and a shift that may result in an increment of activity of central metabolism and the presence of pathogenic genes in both crops.
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Affiliation(s)
- Araceli Lamelas
- Red de Estudios Moleculares Avanzados and Red de Biodiversidad y Sistemática, Instituto de Ecología A. C., Xalapa, Mexico
| | - Damaris Desgarennes
- Red de Estudios Moleculares Avanzados and Red de Biodiversidad y Sistemática, Instituto de Ecología A. C., Xalapa, Mexico
| | - Daniel López-Lima
- Red de Estudios Moleculares Avanzados and Red de Biodiversidad y Sistemática, Instituto de Ecología A. C., Xalapa, Mexico
| | | | - Alexandro Alonso-Sánchez
- Red de Estudios Moleculares Avanzados and Red de Biodiversidad y Sistemática, Instituto de Ecología A. C., Xalapa, Mexico
| | - Alejandro Artacho
- Joint Unit of Research in Genomics and Health, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) and Cavanilles Institute of Biodiversity and Evolutionary Biology, Universitat de València, Valencia, Spain
| | - Amparo Latorre
- Joint Unit of Research in Genomics and Health, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) and Cavanilles Institute of Biodiversity and Evolutionary Biology, Universitat de València, Valencia, Spain
- CIBER en Epidemiología y Salud Pública, Madrid, Spain
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia, Spanish National Research Council (CSIC-UVEG), Valencia, Spain
| | - Andrés Moya
- Joint Unit of Research in Genomics and Health, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) and Cavanilles Institute of Biodiversity and Evolutionary Biology, Universitat de València, Valencia, Spain
- CIBER en Epidemiología y Salud Pública, Madrid, Spain
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia, Spanish National Research Council (CSIC-UVEG), Valencia, Spain
| | - Gloria Carrión
- Red de Estudios Moleculares Avanzados and Red de Biodiversidad y Sistemática, Instituto de Ecología A. C., Xalapa, Mexico
- *Correspondence: Gloria Carrión,
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