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Zhang H, Ma T, Wang L, Yu X, Zhao X, Gao W, Van Zwieten L, Singh BP, Li G, Lin Q, Chadwick DR, Lu S, Xu J, Luo Y, Jones DL, Jeewani PH. Distinct biophysical and chemical mechanisms governing sucrose mineralization and soil organic carbon priming in biochar amended soils: evidence from 10 years of field studies. BIOCHAR 2024; 6:52. [PMID: 38799721 PMCID: PMC11111575 DOI: 10.1007/s42773-024-00327-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 05/29/2024]
Abstract
While many studies have examined the role of biochar in carbon (C) accrual in short-term scale, few have explored the decadal scale influences of biochar on non-biochar C, e.g., native soil organic C (SOC) and added substrate. To address this knowledge gap, soils were collected from decade-old biochar field trials located in the United Kingdom (Cambisol) and China (Fluvisol), with each site having had three application rates (25-30, 50-60 and 75-100 Mg ha-1) of biochar plus an unamended Control, applied once in 2009. We assessed physicochemical and microbial properties associated with sucrose (representing the rhizodeposits) mineralization and the priming effect (PE) on native SOC. Here, we showed both soils amended with biochar at the middle application rate (50 Mg ha-1 biochar in Cambisol and 60 Mg ha-1 biochar in Fluvisol) resulted in greater substrate mineralization. The enhanced accessibility and availability of sucrose to microorganisms, particularly fast-growing bacterial genera like Arenimonas, Spingomonas, and Paenibacillus (r-strategists belonging to the Proteobacteria and Firmicutes phyla, respectively), can be attributed to the improved physicochemical properties of the soil, including pH, porosity, and pore connectivity, as revealed by synchrotron-based micro-CT. Random forest analysis also confirmed the contribution of the microbial diversity and physical properties such as porosity on sucrose mineralization. Biochar at the middle application rate, however, resulted in the lowest PE (0.3 and 0.4 mg of CO2-C g soil-1 in Cambisol and Fluvisol, respectively) after 53 days of incubation. This result might be associated with the fact that the biochar promoted large aggregates formation, which enclosed native SOC in soil macro-aggregates (2-0.25 mm). Our study revealed a diverging pattern between substrate mineralization and SOC priming linked to the biochar application rate. This suggests distinct mechanisms, biophysical and physicochemical, driving the mineralization of non-biochar carbon in a field where biochar was applied a decade before. Supplementary Information The online version contains supplementary material available at 10.1007/s42773-024-00327-0.
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Affiliation(s)
- Haoli Zhang
- College of Land Science and Technology, China Agriculture University, Yuanmingyuan West Road, Beijing, 100193 China
| | - Tao Ma
- Crop Research Institute, Guangxi Agricultural Vocational University, Guangxi, China
| | - Lili Wang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191 China
| | - Xiuling Yu
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058 China
| | - Xiaorong Zhao
- College of Land Science and Technology, China Agriculture University, Yuanmingyuan West Road, Beijing, 100193 China
| | - Weida Gao
- College of Land Science and Technology, China Agriculture University, Yuanmingyuan West Road, Beijing, 100193 China
| | - Lukas Van Zwieten
- NSW Department of Primary Industries, Wollongbar Primary Industries Institute, Wollongbar, NSW 2477 Australia
| | - Bhupinder Pal Singh
- Soils West, Centre for Sustainable Farming Systems, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia
| | - Guitong Li
- College of Land Science and Technology, China Agriculture University, Yuanmingyuan West Road, Beijing, 100193 China
| | - Qimei Lin
- College of Land Science and Technology, China Agriculture University, Yuanmingyuan West Road, Beijing, 100193 China
| | - David R. Chadwick
- School of Environmental and Natural Sciences, Environment Centre Wales, Bangor University, Gwynedd, LL57 2UW UK
| | - Shenggao Lu
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058 China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058 China
| | - Yu Luo
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058 China
| | - David L. Jones
- School of Environmental and Natural Sciences, Environment Centre Wales, Bangor University, Gwynedd, LL57 2UW UK
- Soils West, Centre for Sustainable Farming Systems, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia
| | - Peduruhewa H. Jeewani
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058 China
- School of Environmental and Natural Sciences, Environment Centre Wales, Bangor University, Gwynedd, LL57 2UW UK
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Wang C, Dippold MA, Kuzyakov Y, Dorodnikov M. Microbial strategies for phosphorus acquisition in rice paddies under contrasting water regimes: Multiple source tracing by 32P and 33P. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170738. [PMID: 38325444 DOI: 10.1016/j.scitotenv.2024.170738] [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: 10/07/2023] [Revised: 01/31/2024] [Accepted: 02/04/2024] [Indexed: 02/09/2024]
Abstract
Microbial acquisition and utilization of organic and mineral phosphorus (P) sources in paddy soils are strongly dependent on redox environment and remain the key to understand P turnover and allocation for cell compound synthesis. Using double 32/33P labeling, we traced the P from three sources in a P-limited paddy soil: ferric iron-bound phosphate (Fe-P), wheat straw P (Straw-P), and soil P (Soil-P) in microbial biomass P (MBP) and phospholipids (Phospholipid-P) of individual microbial groups depending on water regimes: (i) continuous flooding or (ii) alternate wetting and drying. 32/33P labeling combined with phospholipid fatty acid analysis allowed to trace P utilization by functional microbial groups. Microbial P nutrition was mainly covered by Soil-P, whereas microorganisms preferred to take up P from mineralized Straw-P than from Fe-P dissolution. The main Straw-P mobilizing agents were Actinobacteria under alternating wetting and drying and other Gram-positive bacteria under continuous flooding. Actinobacteria and arbuscular mycorrhiza increased P incorporation into cell membranes by 1.4-5.8 times under alternate wetting and drying compared to continuous flooding. The Fe-P contribution to MBP was 4-5 times larger in bulk than in rooted soil because (i) rice roots outcompeted microorganisms for P uptake from Fe-P and (ii) rhizodeposits stimulated microbial activity, e.g. phosphomonoesterase production and Straw-P mineralization. Higher phosphomonoesterase activities during slow soil drying compensated for the decreased reductive dissolution of Fe-P. Concluding, microbial P acquisition strategies depend on (i) Soil-P, especially organic P, availability, (ii) the activity of phosphomonoesterases produced by microorganisms and roots, and (iii) P sources - all of which depend on the redox conditions. Maximizing legacy P utilization in the soil as a function of the water regime is one potential way to reduce competition between roots and microbes for P in rice cultivation.
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Affiliation(s)
- Chaoqun Wang
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, 710061 Xi'an, China; Biogeochemistry of Agroecosystems, University of Goettingen, 37077 Goettingen, Germany.
| | - Michaela A Dippold
- Biogeochemistry of Agroecosystems, University of Goettingen, 37077 Goettingen, Germany; Geo-Biosphere Interactions, University of Tuebingen, 72076 Tuebingen, Germany
| | - Yakov Kuzyakov
- Soil Science of Temperate Ecosystems, University of Goettingen, 37077 Goettingen, Germany
| | - Maxim Dorodnikov
- Soil Science of Temperate Ecosystems, University of Goettingen, 37077 Goettingen, Germany; Institute of Landscape Ecology, University of Muenster, 48149 Muenster, Germany
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Benaissa A. Rhizosphere: Role of bacteria to manage plant diseases and sustainable agriculture-A review. J Basic Microbiol 2024; 64:e2300361. [PMID: 37800617 DOI: 10.1002/jobm.202300361] [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: 06/24/2023] [Revised: 09/05/2023] [Accepted: 09/17/2023] [Indexed: 10/07/2023]
Abstract
General plant diseases as well as soil-borne pathogens severely reduce agricultural yield. The rhizosphere (the region of the soil that includes and surrounds the roots) is an important niche for microbial diversity in particular phytobeneficial bacteria including plant growth-promoting rhizobacteria (PGPR) which have been used for a very long time to combat plant diseases. Pathogen control and crop productivity can both be improved through the use of PGPR several mechanisms, including iron-based nutrition, antibiotics, volatile substances, enzymes, biofilm, allelochemicals, and so on. Their modes of action and molecular mechanisms have improved our comprehension of how they are used to control crop disease. Therefore, there is a lot of literal information available regarding PGPR, but this review stands out since it starts with the fundamentals: the concept of the rhizosphere and the colonization process of the latter, particularly because it covers the most mechanisms. A broad figure is used to present the study's findings. The advantages of using PGPR as bioinoculants in sustainable agriculture are also mentioned.
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Affiliation(s)
- Asmaa Benaissa
- Laboratory of Biology and Physiology of Organisms, Faculty of Biological Sciences, University of Sciences and Technology of Houari Boumediene-El-Alia Bab Ezzouar Algiers, Algeria
- Department of Biology, University of Amine Elokkal ElHadj Moussa Eg. Akhamoukh, Sersouf, Tamanrasset, Algeria
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Dos Santos JDN, Pinto E, Martín J, Vicente F, Reyes F, Lage OM. Unveiling the bioactive potential of Actinomycetota from the Tagus River estuary. Int Microbiol 2024:10.1007/s10123-024-00483-0. [PMID: 38236380 DOI: 10.1007/s10123-024-00483-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/28/2023] [Accepted: 01/10/2024] [Indexed: 01/19/2024]
Abstract
The increase in global travel and the incorrect and excessive use of antibiotics has led to an unprecedented rise in antibiotic resistance in bacterial and fungal populations. To overcome these problems, novel bioactive natural products must be discovered, which may be found in underexplored environments, such as estuarine habitats. In the present work, estuarine actinomycetotal strains were isolated with conventional and iChip techniques from the Tagus estuary in Alcochete, Portugal, and analysed for different antimicrobial bioactivities. Extracts were produced from the isolated cultures and tested for bioactivity against Staphylococcus aureus ATCC 29213, Escherichia coli ATCC 25922, Aspergillus fumigatus ATCC 240305, Candida albicans ATCC 10231 and Trichophyton rubrum FF5. Furthermore, bioactive extracts were subjected to dereplication by high-performance liquid chromatography (HPLC) and high-resolution mass spectrometry (HRMS) to putatively identify their chemical components. In total, 105 isolates belonging to 3 genera were obtained. One which was isolated, MTZ3.1 T, represents a described novel taxon for which the name Streptomyces meridianus was proposed. Regarding the bioactivity testing, extracts from 12 strains proved to be active against S. aureus, 2 against E. coli, 4 against A. fumigatus, 3 against C. albicans and 10 against T. rubrum. Dereplication of bioactive extracts showed the presence of 28 known bioactive molecules, 35 hits have one or more possible matches in the DNP and 18 undescribed ones. These results showed that the isolated bacteria might be the source of new bioactive natural products.
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Affiliation(s)
- José Diogo Neves Dos Santos
- Department of Biology, Faculty of Sciences, University of Porto, Rua Do Campo Alegre, S/N, 4169-007, Porto, Portugal.
- Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros Do Porto de Leixões, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal.
| | - Eugénia Pinto
- Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros Do Porto de Leixões, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
- Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Jesús Martín
- Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Fundación MEDINA, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de La Salud, 18016, Granada, Spain
| | - Francisca Vicente
- Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Fundación MEDINA, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de La Salud, 18016, Granada, Spain
| | - Fernando Reyes
- Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Fundación MEDINA, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de La Salud, 18016, Granada, Spain
| | - Olga Maria Lage
- Department of Biology, Faculty of Sciences, University of Porto, Rua Do Campo Alegre, S/N, 4169-007, Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros Do Porto de Leixões, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
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Jian P, Kumano T, Kimura M, Kurisaki M, Hashimoto Y, Kobayashi M. Biodegradation of the methylenedioxyphenyl group in piperine and its derivatives: discovery of a novel methylenetransferase in an actinomycete. Appl Environ Microbiol 2023; 89:e0114523. [PMID: 37874289 PMCID: PMC10686052 DOI: 10.1128/aem.01145-23] [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: 07/04/2023] [Accepted: 09/12/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE Pepper is a spice that has been used worldwide since the Age of Discovery. The substance that is responsible for the spiciness in pepper is piperine, a type of alkaloid. It has never been reported how piperine is degraded by microorganisms. In this study, we discovered a bacterium in the soil that is capable of catabolizing piperine as its sole nitrogen source. Furthermore, we discovered the enzyme involved in piperine metabolism. This enzyme decomposed the methylenedioxyphenyl group, which is the common structure in various plant-derived bioactive compounds such as sesamin, piperonal, safrole, and berberin. By utilizing this enzyme, piperine can be converted into a useful antioxidant compound. The findings about previously unknown metabolic pathways in nature can lead to the discovery of new enzymes and provide methods for the enzymatic synthesis of useful compounds.
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Affiliation(s)
- Pu Jian
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Takuto Kumano
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Mio Kimura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Makoto Kurisaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yoshiteru Hashimoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Michihiko Kobayashi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Center for Quantum and Information Life Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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6
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Barnett SE, Buckley DH. Metagenomic stable isotope probing reveals bacteriophage participation in soil carbon cycling. Environ Microbiol 2023; 25:1785-1795. [PMID: 37139849 DOI: 10.1111/1462-2920.16395] [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: 09/12/2022] [Accepted: 04/25/2023] [Indexed: 05/05/2023]
Abstract
Soil viruses are important components of the carbon (C) cycle, yet we still know little about viral ecology in soils. We added diverse 13 C-labelled carbon sources to soil and we used metagenomic-SIP to detect 13 C assimilation by viruses and their putative bacterial hosts. These data allowed us to link a 13 C-labelled bacteriophage to its 13 C-labelled Streptomyces putative host, and we used qPCR to track the dynamics of the putative host and phage in response to C inputs. Following C addition, putative host numbers increased rapidly for 3 days, and then more gradually, reaching maximal abundance on Day 6. Viral abundance and virus:host ratio increased dramatically over 6 days, and remained high thereafter (8.42 ± 2.94). From Days 6 to 30, virus:host ratio remained high, while putative host numbers declined more than 50%. Putative host populations were 13 C-labelled on Days 3-30, while 13 C-labelling of phage was detected on Days 14 and 30. This dynamic suggests rapid growth and 13 C-labelling of the host fueled by new C inputs, followed by extensive host mortality driven by phage lysis. These findings indicate that the viral shunt promotes microbial turnover in soil following new C inputs, thereby altering microbial community dynamics, and facilitating soil organic matter production.
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Affiliation(s)
- Samuel E Barnett
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Daniel H Buckley
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
- Department of Microbiology, Cornell University, Ithaca, New York, USA
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7
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Nikitina EP, Buyantueva LB, Abidueva EY, Sun CH. Taxonomic and ecophysiological characteristics of actinobacteria in soils of the dry steppe zone of the Selenga Highlands (Western Transbaikalia). Vavilovskii Zhurnal Genet Selektsii 2023; 27:411-420. [PMID: 37465188 PMCID: PMC10350862 DOI: 10.18699/vjgb-23-49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 08/01/2022] [Accepted: 08/03/2022] [Indexed: 07/20/2023] Open
Abstract
Arid habitats have recently attracted increasing attention in terms of biodiversity research and the discovery of new bacterial species. These habitats are among the target ecosystems suitable for isolating new strains of actinobacteria that are likely to produce new metabolites. This paper presents the results on the isolation of actinobacteria from soils of the dry steppe zone of the Selenga Highlands, the characterization of their taxonomic diversity, as well as ecological and trophic properties. The bacterial counts on ISP 4 medium ranged from 6.6 × 105 to 7.1 × 106 CFU/g. The highest bacterial counts were observed in the subsurface and middle horizons of the studied soils. 28 strains of Gram-positive bacteria represented by thin-branched mycelium, coccoid and bacilliform forms were isolated. According to the results of 16S rRNA gene analysis, the isolated strains were representatives of Streptomyces, Arthrobacter, Glycomyces, Kocuria, Microbacterium, Micromonospora, Nocardioides, Pseudarthrobacter, and Rhodococcus (Actinomycetota). One isolate that showed low 16S rRNA gene sequence similarity with previously isolated and validly described species was a new species of the genus Glycomyces. It was shown that all tested strains are mesophilic, prefer neutral or slightly alkaline conditions, have growth limits in the temperature range of 5-45 °C and pH 6-9. The optimal NaCl concentration for growth of most strains was 0-1 %. The strains under study were capable of utilizing a wide range of mono- and disaccharides and polyatomic alcohols as a carbon source. The isolated strains were capable of using both organic (proteins and amino acids) and inorganic (ammonium salts and nitrates) compounds as nitrogen sources. The examinations of extracellular enzymes showed that all isolates were capable of producing catalase and amylase; 78.6 % of the total number of isolates produced protease and lipase; 53.6 %, cellulase; and 28.6 %, urease. The data obtained expand current knowledge about the diversity of microbial communities in soils of the Selenga Highlands and also confirm the potential of searching for new actinobacteria species in these soils.
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Affiliation(s)
- E P Nikitina
- Baikal Institute of Nature Management of the Siberian Branch of the Russian Academy of Sciences, Ulan-Ude, Russia Banzarov Buryat State University, Ulan-Ude, Russia
| | | | - E Yu Abidueva
- Institute of General and Experimental Biology of the Siberian Branch of the Russian Academy of Sciences, Ulan-Ude, Russia
| | - C H Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, China
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8
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González Plaza JJ, Hradecký J. The tropical cookbook: Termite diet and phylogenetics—Over geographical origin—Drive the microbiome and functional genetic structure of nests. Front Microbiol 2023; 14:1089525. [PMID: 36998409 PMCID: PMC10043212 DOI: 10.3389/fmicb.2023.1089525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/13/2023] [Indexed: 03/15/2023] Open
Abstract
Termites are key decomposers of dead plant material involved in the organic matter recycling process in warm terrestrial ecosystems. Due to their prominent role as urban pests of timber, research efforts have been directed toward biocontrol strategies aimed to use pathogens in their nest. However, one of the most fascinating aspects of termites is their defense strategies that prevent the growth of detrimental microbiological strains in their nests. One of the controlling factors is the nest allied microbiome. Understanding how allied microbial strains protect termites from pathogen load could provide us with an enhanced repertoire for fighting antimicrobial-resistant strains or mining for genes for bioremediation purposes. However, a necessary first step is to characterize these microbial communities. To gain a deeper understanding of the termite nest microbiome, we used a multi-omics approach for dissecting the nest microbiome in a wide range of termite species. These cover several feeding habits and three geographical locations on two tropical sides of the Atlantic Ocean known to host hyper-diverse communities. Our experimental approach included untargeted volatile metabolomics, targeted evaluation of volatile naphthalene, a taxonomical profile for bacteria and fungi through amplicon sequencing, and further diving into the genetic repertoire through a metagenomic sequencing approach. Naphthalene was present in species belonging to the genera Nasutitermes and Cubitermes. We investigated the apparent differences in terms of bacterial community structure and discovered that feeding habits and phylogenetic relatedness had a greater influence than geographical location. The phylogenetic relatedness among nests' hosts influences primarily bacterial communities, while diet influences fungi. Finally, our metagenomic analysis revealed that the gene content provided both soil-feeding genera with similar functional profiles, while the wood-feeding genus showed a different one. Our results indicate that the nest functional profile is largely influenced by diet and phylogenetic relatedness, irrespective of geographical location.
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9
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Genomic Investigation of Desert Streptomyces huasconensis D23 Reveals Its Environmental Adaptability and Antimicrobial Activity. Microorganisms 2022; 10:microorganisms10122408. [PMID: 36557661 PMCID: PMC9784485 DOI: 10.3390/microorganisms10122408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The harsh climatic conditions of deserts may lead to unique adaptations of microbes, which could serve as potential sources of new metabolites to cope with environmental stresses. However, the mechanisms governing the environmental adaptability and antimicrobial activity of desert Streptomyces remain inadequate, especially in extreme temperature differences, drought conditions, and strong radiation. Here, we isolated a Streptomyces strain from rocks in the Kumtagh Desert in Northwest China and tested its antibacterial activity, resistance to UV-C irradiation, and tolerance to hydrogen peroxide (H2O2). The whole-genome sequencing was carried out to study the mechanisms underlying physiological characteristics and ecological adaptation from a genomic perspective. This strain has a growth inhibitory effect against a variety of indicator bacteria, and the highest antibacterial activity recorded was against Bacillus cereus. Moreover, strain D23 can withstand UV-C irradiation up to 100 J/m2 (D10 = 80 J/m2) and tolerate stress up to 70 mM H2O2. The genome prediction of strain D23 revealed the mechanisms associated with its adaptation to extreme environmental and stressful conditions. In total, 33 biosynthetic gene clusters (BGCs) were predicted based on anti-SMASH. Gene annotation found that S. huasconensis D23 contains several genes and proteins associated with the biosynthesis of factors required to cope with environmental stress of temperature, UV radiation, and osmotic pressure. The results of this study provide information about the genome and BGCs of the strain S. huasconensis D23. The experimental results combined with the genome sequencing data show that antimicrobial activity and stress resistance of S. huasconensis D23 was due to the rich and diverse secondary metabolite production capacity and the induction of stress-responsive genes. The environmental adaptability and antimicrobial activity information presented here will be valuable for subsequent work regarding the isolation of bioactive compounds and provide insight into the ecological adaptation mechanism of microbes to extreme desert environments.
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10
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Qu ZL, Li XL, Ge Y, Palviainen M, Zhou X, Heinonsalo J, Berninger F, Pumpanen J, Köster K, Sun H. The impact of biochar on wood-inhabiting bacterial community and its function in a boreal pine forest. ENVIRONMENTAL MICROBIOME 2022; 17:45. [PMID: 36042528 PMCID: PMC9429645 DOI: 10.1186/s40793-022-00439-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 08/22/2022] [Indexed: 05/31/2023]
Abstract
Biochar is considered to be a possible means of carbon sequestration to alleviate climate change. However, the dynamics of the microbial community during wood decomposition after biochar application remain poorly understood. In this study, the wood-inhabiting bacterial community composition and its potential functions during a two-year decomposition period after the addition of different amounts of biochar (0.5 kg m-2 and 1.0 kg m-2), and at different biochar pyrolysis temperatures (500 °C and 650 °C), in a boreal Scots pine forest, were analyzed using Illumina NovaSeq sequencing combined with Functional Annotation of Prokaryotic Taxa (FAPROTAX). The results showed that the wood decomposition rates increased after biochar addition to the soil surface in the second year. Treatment with biochar produced at high temperatures increased the diversity of wood-inhabiting bacteria more than that produced at low temperatures (P < 0.05). The wood-inhabiting bacterial diversity and species richness decreased with decomposition time. The biochar treatments changed the wood-inhabiting bacterial community structure during the decomposition period. The pyrolysis temperature and the amount of applied biochar had no effect on the bacterial community structure but shifted the abundance of certain bacterial taxa. Similarly, biochar application shifted the wood-inhabiting bacterial community function in the first year, but not in the second year. The wood-inhabiting bacterial community and function were affected by soil pH, soil water content, and soil total nitrogen. The results provide useful information on biochar application for future forest management practices. Long-term monitoring is needed to better understand the effects of biochar application on nutrient cycling in boreal forests.
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Affiliation(s)
- Zhao-Lei Qu
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiao-Li Li
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Yan Ge
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Marjo Palviainen
- Department of Forest Sciences, University of Helsinki, Latokartanonkaari 7, P.O. Box 27, 00014, Helsinki, Finland
| | - Xuan Zhou
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1 E, P. O. Box 1627, 70211, Kuopio, Finland
| | - Jussi Heinonsalo
- Department of Forest Sciences, University of Helsinki, Latokartanonkaari 7, P.O. Box 27, 00014, Helsinki, Finland
| | - Frank Berninger
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1 E, P. O. Box 1627, 70211, Kuopio, Finland
| | - Jukka Pumpanen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1 E, P. O. Box 1627, 70211, Kuopio, Finland
| | - Kajar Köster
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1 E, P. O. Box 1627, 70211, Kuopio, Finland
| | - Hui Sun
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.
- Department of Forest Sciences, University of Helsinki, Latokartanonkaari 7, P.O. Box 27, 00014, Helsinki, Finland.
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11
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Krysenko S, Wohlleben W. Polyamine and Ethanolamine Metabolism in Bacteria as an Important Component of Nitrogen Assimilation for Survival and Pathogenicity. Med Sci (Basel) 2022; 10:40. [PMID: 35997332 PMCID: PMC9397018 DOI: 10.3390/medsci10030040] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
Nitrogen is an essential element required for bacterial growth. It serves as a building block for the biosynthesis of macromolecules and provides precursors for secondary metabolites. Bacteria have developed the ability to use various nitrogen sources and possess two enzyme systems for nitrogen assimilation involving glutamine synthetase/glutamate synthase and glutamate dehydrogenase. Microorganisms living in habitats with changeable availability of nutrients have developed strategies to survive under nitrogen limitation. One adaptation is the ability to acquire nitrogen from alternative sources including the polyamines putrescine, cadaverine, spermidine and spermine, as well as the monoamine ethanolamine. Bacterial polyamine and monoamine metabolism is not only important under low nitrogen availability, but it is also required to survive under high concentrations of these compounds. Such conditions can occur in diverse habitats such as soil, plant tissues and human cells. Strategies of pathogenic and non-pathogenic bacteria to survive in the presence of poly- and monoamines offer the possibility to combat pathogens by using their capability to metabolize polyamines as an antibiotic drug target. This work aims to summarize the knowledge on poly- and monoamine metabolism in bacteria and its role in nitrogen metabolism.
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Affiliation(s)
- Sergii Krysenko
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Department of Microbiology and Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany;
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, 72076 Tübingen, Germany
| | - Wolfgang Wohlleben
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Department of Microbiology and Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany;
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, 72076 Tübingen, Germany
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12
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Das P, Kundu S, Maiti PK, Mandal S, Sahoo P, Mandal S. An antibacterial compound pyrimidomycin produced by Streptomyces sp. PSAA01 isolated from soil of Eastern Himalayan foothill. Sci Rep 2022; 12:10176. [PMID: 35715695 PMCID: PMC9206078 DOI: 10.1038/s41598-022-14549-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/08/2022] [Indexed: 11/10/2022] Open
Abstract
Selective isolation of soil Actinobacteria was undertaken to isolate a new class of antibiotics and bioactive molecules. A Streptomyces sp. PSAA01 (= MTCC 13,157), isolated from soil of Eastern Himalaya foothill was cultivated on a large scale for the production of the antimicrobial SM02. It has been found that the maximum amount of SM02 produced while PSAA01 was grown in ISP-2 medium (pH 7.0) for 7 days at 30 °C in shaking (180 rpm) condition. A significant zone of inhibition against Staphylococcus aureus MTCC 96 has been found with the crude cell-free culture media (50 µL) of 7 days grown PSAA01. After the purification and chemical structural characterization, we found that SM02 is a new antimicrobial having 746 dalton molecular weight. The compound SM02 contains pyrimidine moiety in it and is produced by a species of Streptomyces and thus we have named this antibiotic pyrimidomycin. The antimicrobial spectrum of pyrimidomycin has been found to be restricted in Gram-positive organisms with a MIC of 12 µg/mL. SM02 was found active against Mycobacterium sp. and also multi-drug resistant Gram-positive bacteria with similar potency and found to disrupt the bacterial cell wall. Pyrimidomycin also showed significant impairment in the biofilm formation by S. aureus. Furthermore, pyrimidomycin showed synergy with the most used antibiotic like ampicillin, vancomycin and chloramphenicol. Pyrimidomycin did not have cytotoxicity towards human cell lines indicating its limited activity within bacteria.
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Affiliation(s)
- Prasenjit Das
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Shampa Kundu
- The Molecular Recognition Laboratory, Department of Chemistry, Visva-Bharati University, Siksha Bhavana, Santiniketan, Birbhum, West Bengal, 731235, India
| | - Pulak Kumar Maiti
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Saurodeep Mandal
- The Molecular Recognition Laboratory, Department of Chemistry, Visva-Bharati University, Siksha Bhavana, Santiniketan, Birbhum, West Bengal, 731235, India
| | - Prithidipa Sahoo
- The Molecular Recognition Laboratory, Department of Chemistry, Visva-Bharati University, Siksha Bhavana, Santiniketan, Birbhum, West Bengal, 731235, India.
| | - Sukhendu Mandal
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India.
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13
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Streptomycetaceae and Promicromonosporaceae: Two Actinomycetes Families from Moroccan Oat Soils Enhancing Solubilization of Natural Phosphate. Microorganisms 2022; 10:microorganisms10061116. [PMID: 35744634 PMCID: PMC9230749 DOI: 10.3390/microorganisms10061116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/21/2022] [Accepted: 05/26/2022] [Indexed: 11/17/2022] Open
Abstract
Soil actinomycetes explorations appear to be an efficient alternative as biofertilizers to optimize the use of phosphorus (P) resources and enhance plant growth. This research aimed to explore the distribution of actinomycetes isolated from four different rhizospheric Moroccan oat soils and to investigate their potential for P solubilization. The distribution of actinomycetes was significantly more abundant in Settat (9.68%), Tangier (7.38%), and Beni Mellal (6.87%) than in the Merchouch-Rabat (4.90%) region. A total of 235 actinomycete strains were isolated from all sites and tested for their ability to grow on a synthetic minimum medium (SMM) containing insoluble natural rock phosphate (RP) or synthetic tricalcium phosphate (TCP) as the unique P source. One hundred forty-three isolates (60.8%) had the ability to grow in the SMM with RP whereas only twenty-five isolates (17%) had the most active growth using the SMM with TCP. Eight isolates with the most active growth in solid SMM were selected for their P solubilization abilities in liquid SMM cultures. The highest amount of P solubilized was 163.8 µg/mL for RP and 110.27 µg/mL for TCP after 5 days of culture. The biosolubilization process of AM2, the most efficient RP and TCP solubilizing strain, probably implied the highest excretion of siderophore substances. Eight of these strains were shown to belong to the Streptomyces genus and one to the Promicromonospora genus. These findings bolster the phosphate biosolubilization abilities of actinomycetes and may participate in increasing agricultural yields in an eco-efficient and environmentally friendly manner.
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14
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Xing L, Xia YY, Zhang QY, Xia ZF, Wan CX, Zhang LL, Luo XX. Streptomyces griseicoloratus sp. nov., isolated from soil in cotton fields in Xinjiang, China. Arch Microbiol 2022; 204:254. [PMID: 35412082 DOI: 10.1007/s00203-022-02818-9] [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: 02/02/2021] [Revised: 01/26/2022] [Accepted: 02/15/2022] [Indexed: 11/29/2022]
Abstract
A novel bacterium of the genus Streptomyces, designated TRM S81-3T, was isolated from soil in cotton fields of Xinjiang, China. Comparative 16S rRNA gene sequence analysis indicated that strain TRM S81-3T is most closely related to Streptomyces viridiviolaceus NBRC 13359T (98.9% sequence similarity); however, the average nucleotide identity (ANI) between strains TRM S81-3T and S. viridiviolaceus NBRC 13359T is relatively low (91.6%). Strain TRM S81-3T possesses LL-diaminopimelic acid as the diagnostic cell-wall diamino acid, MK-9(H4), MK-9(H6), and MK-9(H10) as the major menaquinones, and polar lipids including diphosphatidylglycerol (DPG), phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylmethyl ethanolamine (PME), phosphotidylinositolone (PI), phospholipid of unknown structure containing glucosamine (NPG), and two unidentified phospholipids (PLs).The major fatty acids are iso-C16:0, anteiso-C15:0, anteiso-C17:1 ω9c, anteiso-C17:0, iso-C15:0, and C14:0. The genomic DNA G + C content is 72.1%. Based on the evidence from this polyphasic study, strain TRM S81-3T represents a novel species of Streptomyces, for which the name Streptomyces grisecoloratus is proposed. The type strain is TRM S81-3T (= CCTCC AA 2020002T = LMG 31942T).
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Affiliation(s)
- Li Xing
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps/College of Life Science, Tarim University, Alar, 843300, People's Republic of China
| | - Ying-Ying Xia
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps/College of Life Science, Tarim University, Alar, 843300, People's Republic of China
| | - Qiao-Yan Zhang
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps/College of Life Science, Tarim University, Alar, 843300, People's Republic of China
| | - Zhan-Feng Xia
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps/College of Life Science, Tarim University, Alar, 843300, People's Republic of China.
| | - Chuan-Xing Wan
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps/College of Life Science, Tarim University, Alar, 843300, People's Republic of China
| | - Li-Li Zhang
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps/College of Life Science, Tarim University, Alar, 843300, People's Republic of China
| | - Xiao-Xia Luo
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps/College of Life Science, Tarim University, Alar, 843300, People's Republic of China.
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15
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Davies-Bolorunduro OF, Ajayi A, Adeleye IA, Kristanti AN, Aminah NS. Bioprospecting for antituberculosis natural products – A review. OPEN CHEM 2021. [DOI: 10.1515/chem-2021-0095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Abstract
There has been an increase in the reported cases of tuberculosis, a disease caused by Mycobacterium tuberculosis, which is still currently affecting most of the world’s population, especially in resource-limited countries. The search for novel antitubercular chemotherapeutics from underexplored natural sources is therefore of paramount importance. The renewed interest in studies related to natural products, driven partly by the growing incidence of MDR-TB, has increased the prospects of discovering new antitubercular drug leads. This is because most of the currently available chemotherapeutics such as rifampicin and capreomycin used in the treatment of TB were derived from natural products, which are proven to be an abundant source of novel drugs used to treat many diseases. To meet the global need for novel antibiotics from natural sources, various strategies for high-throughput screening have been designed and implemented. This review highlights the current antitubercular drug discovery strategies from natural sources.
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Affiliation(s)
- Olabisi Flora Davies-Bolorunduro
- Centre for Tuberculosis Research, Nigerian Institute of Medical Research , Yaba , Lagos , Nigeria
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga , Surabaya , Indonesia
| | - Abraham Ajayi
- Molecular Biology and Biotechnology Department, Nigerian Institute of Medical Research , Yaba , Lagos , Nigeria
- Department of Microbiology, University of Lagos , Akoka , Lagos , Nigeria
| | | | - Alfinda Novi Kristanti
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga , Surabaya , Indonesia
- Biotechnology of Tropical Medicinal Plants Research Group, Universitas Airlangga , Surabaya , Indonesia
| | - Nanik Siti Aminah
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga , Surabaya , Indonesia
- Biotechnology of Tropical Medicinal Plants Research Group, Universitas Airlangga , Surabaya , Indonesia
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16
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Grinter R, Greening C. Cofactor F420: an expanded view of its distribution, biosynthesis and roles in bacteria and archaea. FEMS Microbiol Rev 2021; 45:fuab021. [PMID: 33851978 PMCID: PMC8498797 DOI: 10.1093/femsre/fuab021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/11/2021] [Indexed: 12/11/2022] Open
Abstract
Many bacteria and archaea produce the redox cofactor F420. F420 is structurally similar to the cofactors FAD and FMN but is catalytically more similar to NAD and NADP. These properties allow F420 to catalyze challenging redox reactions, including key steps in methanogenesis, antibiotic biosynthesis and xenobiotic biodegradation. In the last 5 years, there has been much progress in understanding its distribution, biosynthesis, role and applications. Whereas F420 was previously thought to be confined to Actinobacteria and Euryarchaeota, new evidence indicates it is synthesized across the bacterial and archaeal domains, as a result of extensive horizontal and vertical biosynthetic gene transfer. F420 was thought to be synthesized through one biosynthetic pathway; however, recent advances have revealed variants of this pathway and have resolved their key biosynthetic steps. In parallel, new F420-dependent biosynthetic and metabolic processes have been discovered. These advances have enabled the heterologous production of F420 and identified enantioselective F420H2-dependent reductases for biocatalysis. New research has also helped resolve how microorganisms use F420 to influence human and environmental health, providing opportunities for tuberculosis treatment and methane mitigation. A total of 50 years since its discovery, multiple paradigms associated with F420 have shifted, and new F420-dependent organisms and processes continue to be discovered.
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Affiliation(s)
- Rhys Grinter
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Chris Greening
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
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17
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Davies-Bolorunduro O, Osuolale O, Saibu S, Adeleye I, Aminah N. Bioprospecting marine actinomycetes for antileishmanial drugs: current perspectives and future prospects. Heliyon 2021; 7:e07710. [PMID: 34409179 PMCID: PMC8361068 DOI: 10.1016/j.heliyon.2021.e07710] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/25/2021] [Accepted: 07/30/2021] [Indexed: 01/01/2023] Open
Abstract
Revived analysis interests in natural products in the hope of discovering new and novel antileishmanial drug leads have been driven partially by the increasing incidence of drug resistance. However, the search for novel chemotherapeutics to combat drug resistance had previously concentrated on the terrestrial environment. As a result, the marine environment was often overlooked. For example, actinomycetes are an immensely important group of bacteria for antibiotic production, producing two-thirds of the known antibiotics. However, these bacteria have been isolated primarily from terrestrial sources. Consequently, there have been revived efforts to discover new compounds from uncharted or uncommon environments like the marine ecosystem. Isolation, purification and structure elucidation of target compounds from complex metabolic extract are major challenges in natural products chemistry. As a result, marine-derived natural products from actinomycetes that have antileishmanial bioactivity potentials have been understudied. This review highlights metagenomic and bioassay approaches which could help streamline the drug discovery process thereby greatly reducing time and cost of dereplication to identify suitable antileishmanial drug candidates.
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Affiliation(s)
- O.F. Davies-Bolorunduro
- Microbiology Department, Nigerian Institute of Medical Research, Lagos, Nigeria
- Postdoc Fellow Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Komplek Kampus C, Jl. Mulyorejo, Surabaya, 60115, Indonesia
| | - O. Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research Group (AEMIDR), Department of Biological Sciences, Elizade University, Ilara Mokin, Nigeria
| | - S. Saibu
- Department of Microbiology, University of Lagos, Akoka, Lagos, Nigeria
| | - I.A. Adeleye
- Department of Microbiology, University of Lagos, Akoka, Lagos, Nigeria
| | - N.S. Aminah
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Komplek Kampus C UNAIR, Jl. Mulyorejo, Surabaya, 60115, Indonesia
- Biotechnology of Tropical Medicinal Plants Research Group, Universitas Airlangga, Indonesia
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18
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Perreault L, Forrester JA, Mladenoff DJ, Lewandowski TE. Deadwood Reduces the Variation in Soil Microbial Communities Caused by Experimental Forest Gaps. Ecosystems 2021. [DOI: 10.1007/s10021-021-00624-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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19
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Liu S, Wang T, Lu Q, Li F, Wu G, Jiang Z, Habden X, Liu L, Zhang X, Lukianov DA, Osterman IA, Sergiev PV, Dontsova OA, Sun C. Bioprospecting of Soil-Derived Actinobacteria Along the Alar-Hotan Desert Highway in the Taklamakan Desert. Front Microbiol 2021; 12:604999. [PMID: 33790875 PMCID: PMC8005632 DOI: 10.3389/fmicb.2021.604999] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/22/2021] [Indexed: 02/04/2023] Open
Abstract
Taklamakan desert is known as the largest dunefield in China and as the second largest shifting sand desert in the world. Although with long history and glorious culture, the Taklamakan desert remains largely unexplored and numerous microorganisms have not been harvested in culture or taxonomically identified yet. The main objective of this study is to explore the diversity, novelty, and pharmacological potential of the cultivable actinomycetes from soil samples at various sites along the Alar-Hotan desert highway in the Taklamakan desert. A total of 590 actinobacterial strains were recovered by the culture-dependent approach. Phylogenetic analysis based on 16S ribosomal RNA (rRNA) gene sequences unveiled a significant level of actinobacterial diversity with 55 genera distributed in 27 families of 12 orders. Thirty-six strains showed relatively low 16S rRNA similarities (<98.65%) with validly described species, among which four strains had already been characterized as novel taxa by our previous research. One hundred and forty-six actinobacterial isolates were selected as representatives to evaluate the antibacterial activities and mechanism of action by the paper-disk diffusion method and a double fluorescent protein reporter "pDualrep2" system, respectively. A total of 61 isolates exhibited antagonistic activity against the tested "ESKAPE" pathogens, among which seven strains could produce bioactive metabolites either to be able to block translation machinery or to induce SOS-response in the pDualrep2 system. Notably, Saccharothrix sp. 16Sb2-4, harboring a promising antibacterial potential with the mechanism of interfering with protein translation, was analyzed in detail to gain deeper insights into its bioactive metabolites. Through ultra-performance liquid chromatography (UPLC)-quadrupole time-of-flight (QToF)-MS/MS based molecular networking analysis and databases identification, four families of compounds (1-16) were putatively identified. Subsequent bioassay-guided separation resulted in purification of four 16-membered macrolide antibiotics, aldgamycin H (8), aldgamycin K (9), aldgamycin G (10), and swalpamycin B (11), and their structures were elucidated by HR-electrospray ionization source (ESI)-MS and NMR spectroscopy. All compounds 8-11 displayed antibacterial activities by inhibiting protein synthesis in the pDualrep2 system. In conclusion, this work demonstrates that Taklamakan desert is a potentially unique reservoir of versatile actinobacteria, which can be a promising source for discovery of novel species and diverse bioactive compounds.
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Affiliation(s)
- Shaowei Liu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ting Wang
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qinpei Lu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Feina Li
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Gang Wu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhongke Jiang
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xugela Habden
- College of Life Science, Xinjiang Normal University, Urumchi, China
| | - Lin Liu
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xiaolin Zhang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Dmitry A. Lukianov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Ilya A. Osterman
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Petr V. Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Olga A. Dontsova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Chenghang Sun
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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20
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Zhang QY, Qin S, Luo XX, Xia ZF. Streptomyces gossypiisoli sp. nov., isolated from cotton soil in Xinjiang, PR China. Int J Syst Evol Microbiol 2020; 71. [PMID: 33269996 DOI: 10.1099/ijsem.0.004561] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinobacterium, designated TRM 44567T, was isolated from cotton soil in Xinjiang Uygur Autonomous Region, northwest PR China. Growth occurred at 16-45 °C, pH 5.0-9.0, and 0-7 % (w/v) NaCl, with optimum growth at 37 °C, pH 7.0-8.0 and 1 % (w/v) NaCl, respectively. Comparative 16S rRNA gene sequence analysis indicated that strain TRM 44567T was phylogenetically most closely related to Streptomyces chromofuscus NBRC 12851T (98.48 % sequence similarity); however, the average nucleotide identity between strain TRM 44567T and S. chromofuscus NBRC 12851T was only 83.77 %. Strain TRM 44567T possessed ll-diaminopimelic acid as the diagnostic cell-wall diamino acid. The predominant menaquinones were MK-9(H10), MK-9(H6) and MK-9(H4). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol and phosphatidylinositol mannoside. The major fatty acids were iso-C16 : 0, C16 : 0, anteiso-C15 : 0, anteiso-C17 : 0, iso-C14 : 0 and iso-C15 : 0. The genomic DNA G+C content was 70.8 mol%. Strain TRM 44567T represents a novel species of the genus Streptomyces, for which the name Streptomyces gossypiisoli sp. nov. is proposed. The type strain is TRM 44567T (=KCTC 39957 T=CCTCC AA 2017011T).
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Affiliation(s)
- Qiao-Yan Zhang
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin /College of Life Science, Tarim University, Alar 843300, PR China
| | - Song Qin
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin /College of Life Science, Tarim University, Alar 843300, PR China
| | - Xiao-Xia Luo
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin /College of Life Science, Tarim University, Alar 843300, PR China
| | - Zhan-Feng Xia
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin /College of Life Science, Tarim University, Alar 843300, PR China
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21
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Hamid ME, Mahgoub A, Babiker AJO, Babiker HAE, Holie MAI, Elhassan MM, Joseph MRP. Isolation and Identification of Streptomyces spp. from Desert and Savanna Soils in Sudan. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17238749. [PMID: 33255614 PMCID: PMC7734577 DOI: 10.3390/ijerph17238749] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/23/2020] [Accepted: 11/12/2020] [Indexed: 12/17/2022]
Abstract
The purpose of this study was to investigate streptomycete populations in desert and savanna ecozones in Sudan and to identify species based on 16S rRNA gene sequences. A total of 49 different Streptomyces phenotypes (22 from sites representing the desert and semi-desert ecozone; 27 representing the savanna ecozone) have been included in the study. The isolates were characterized phenotypically and confirmed using 16S rRNA gene sequence analysis. The two ecozones showed both similarities and uniqueness in the types of isolates. The shared species were in cluster 1 (Streptomyces (S.) werraensis), cluster 2 (Streptomyces sp.), cluster 3 (S. griseomycini-like), and cluster 7 (S. rochei). The desert ecozone revealed unique species in cluster 9 (Streptomyces sp.) and cluster 10 (S. griseomycini). Whereas, the savanna ecozone revealed unique species in cluster 4 (Streptomyces sp.), cluster 5 (S. albogriseolus/ S. griseoincarnatus), cluster 6 (S. djakartensis), and cluster 8 (Streptomyces sp.). Streptomycetes are widely distributed in both desert and the savanna ecozones and many of these require full descriptions. Extending knowledge on Streptomyces communities and their dynamics in different ecological zones and their potential antibiotic production is needed.
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Affiliation(s)
- Mohamed E. Hamid
- Department of Clinical Microbiology and Parasitology, College of Medicine, King Khalid University, P.O. Box 641, Abha 61314, Saudi Arabia;
- Department of Preventive Medicine, Faculty of Veterinary Medicine, University of Khartoum, Khartoum North 13314, Sudan;
- Correspondence: ; Tel.: +966-5-0977-3687
| | - Adil Mahgoub
- Department of Preventive Medicine, Faculty of Veterinary Medicine, University of Khartoum, Khartoum North 13314, Sudan;
- Department of Microbiology, College of Medical Laboratory Science, Alzeim Alazhari University, Khartoum North 12217, Sudan;
| | | | - Hussein A. E. Babiker
- Department of Clinical Science, College of Veterinary Medicine, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia;
| | - Mohammed A. I. Holie
- Department of Microbiology, College of Medical Laboratory Science, Alzeim Alazhari University, Khartoum North 12217, Sudan;
| | - Mogahid M. Elhassan
- Department of Clinical Laboratory Science, College of Applied Medical Science, Taibah University, Al-Madinah 13215, Saudi Arabia;
| | - Martin R. P. Joseph
- Department of Clinical Microbiology and Parasitology, College of Medicine, King Khalid University, P.O. Box 641, Abha 61314, Saudi Arabia;
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Soil quality parameters vis-a-vis growth and yield attributes of sugarcane as influenced by integration of microbial consortium with NPK fertilizers. Sci Rep 2020; 10:19180. [PMID: 33154431 PMCID: PMC7645686 DOI: 10.1038/s41598-020-75829-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/16/2020] [Indexed: 11/23/2022] Open
Abstract
Intensive agriculture involving high crop intensity, unavailability of organics, and higher use of straight fertilizers causes imbalanced use and deficiencies of several other macro and micronutrients. Nutrients supply through the integration of microbial consortium containing Gluconacetobater diazotrophicus, Trichoderma harzianum, and Pseudomonas fluorescens can reduce the requirements on the one hand and can also increase the response of chemical fertilizers. Thus we had planned the present experiment with the objectives (i) to determine the effect of integrated application of microbial consortium (MC) and NPK fertilizer on soil quality parameters and crop growth and yield attributes and (ii) to assess the effect of integration on agronomic efficiency of N, P and K and find out the possibilities for reduction in applied doses of NPK, if any. Five treatments viz., T1; N0P0K0; T2: N75P13K25; T3: N150P26K50; T4: N75P13K25 + microbial consortium and T5: N150P26K50 + microbial consortium containing new strains of Trichoderma harzianum, Gluconcetobacter diazotrophicus, and Pseudomonas fluorescens (CFU 109–10 per ml liquid culture) were evaluated under four replications in a randomized block design (RBD). Experimental results indicated that integrating microbial consortium and NPK fertilizers' application proved effective in improving soil organic carbon, soil microbial population, microbial biomass carbon, microbial biomass nitrogen, and soil respiration. Integrated use of microbial consortium with NPK also improved the cation exchange capacity of soil and roots. However, the growth and yield attributes, nutrients uptake, sugarcane, and sugar yields also revealed a positive effect of microbial consortium's integrated application with NPK. The integration of MC and NPK also improved the agronomic efficiency of applied nutrients (NPK). Reduction of 50% NPK with these microbial consortia (Trichoderma harzianum, Gluconcetobacter diazotrophicus, and Pseudomonas fluorescens) was found better than the application of full NPK through chemical fertilizers. Thus application of N150P26K50 with microbial consortium can sustain soil fertility besides improving sugarcane and sugar yields in subtropical Indian conditions.
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Willing CE, Pierroz G, Coleman-Derr D, Dawson TE. The generalizability of water-deficit on bacterial community composition; Site-specific water-availability predicts the bacterial community associated with coast redwood roots. Mol Ecol 2020; 29:4721-4734. [PMID: 33000868 DOI: 10.1111/mec.15666] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/01/2022]
Abstract
Experimental drought has been shown to delay the development of the root microbiome and increase the relative abundance of Actinobacteria, however, the generalizability of these findings to natural systems or other diverse plant hosts remains unknown. Bacterial cell wall thickness and growth morphology (e.g., filamentous or unicellular) have been proposed as traits that may mediate bacterial responses to environmental drivers. Leveraging a natural gradient of water-availability across the coast redwood (Sequoia sempervirens) range, we tested three hypotheses: (a) that site-specific water-availability is an important predictor of bacterial community composition for redwood roots and rhizosphere soils; (b) that there is relative enrichment of Actinobacteria and other monoderm bacterial groups within the redwood microbiome in response to drier conditions; and (c) that bacterial growth morphology is an important predictor of bacteria response to water-availability, where filamentous taxa will become more dominant at drier sites compared to unicellular bacteria. We find that both α- and β-diversity of redwood bacterial communities is partially explained by water-availability and that Actinobacterial enrichment is a conserved response of land plants to water-deficit. Further, we highlight how the trend of Actinobacterial enrichment in the redwood system is largely driven by the Actinomycetales. We propose bacterial growth morphology (filamentous vs. unicellular) as an additional mechanism behind the increase in Actinomycetales with increasing aridity. A trait-based approach including cell-wall thickness and growth morphology may explain the distribution of bacterial taxa across environmental gradients and help to predict patterns of bacterial community composition for a wide range of host plants.
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Affiliation(s)
- Claire E Willing
- Department of Environmental Science, Policy and Management, UC Berkeley, Berkeley, CA, USA
| | - Grady Pierroz
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, USA.,Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
| | - Devin Coleman-Derr
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, USA.,Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
| | - Todd E Dawson
- Department of Environmental Science, Policy and Management, UC Berkeley, Berkeley, CA, USA.,Department of Integrative Biology, UC Berkeley, Berkeley, CA, USA
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24
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Daws SC, Cline LA, Rotenberry J, Sadowsky MJ, Staley C, Dalzell B, Kennedy PG. Do shared traits create the same fates? Examining the link between morphological type and the biogeography of fungal and bacterial communities. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100948] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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25
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Abstract
Microbial diversity has been well documented for the top 0–0.30 m of agricultural soils. However, spatio-temporal research into subsoil microbial diversity and the effects of agricultural management remains limited. Soil type may influence subsoil microbial diversity, particularly Vertosols. These soils lack distinct horizons and are known to facilitate the downward movement of organic matter, potentially supporting subsoil microbiota, removed from the crop root system (i.e., bulk soils). Our research used the MiSeq Illumina Platform to investigate microbial diversity down the profile of an agricultural Australian Vertosol to 1.0 m in bulk soils, as influenced by crop system (continuous cotton and cotton–maize) and sample time (pre- and in-crop samples collected over two seasons). Overall, both alpha- (Chao1, Gini–Simpson Diversity and Evenness indices) and beta-diversity (nMDS and Sørensen’s Index of Similarity) metrics indicated that both bacterial (16S) diversity and fungal (ITS) diversity decreased with increasing soil depth. The addition of a maize rotation did not significantly influence alpha-diversity metrics until 0.70–1.0 m depth in the soil, where bacterial diversity was significantly higher in this system, with beta-diversity measures indicating this is likely due to root system differences influencing dissolved organic carbon. Sample time did not significantly affect bacterial or fungal diversity over the two seasons, regardless of the crop type and status (i.e., crop in ground and post crop). The relatively stable subsoil fungal and overall microbial diversity in bulk soils over two crop seasons suggests that these microbiota have developed a tolerance to prolonged agricultural management.
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Genome-scale metabolic models of Microbacterium species isolated from a high altitude desert environment. Sci Rep 2020; 10:5560. [PMID: 32221328 PMCID: PMC7101325 DOI: 10.1038/s41598-020-62130-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 02/28/2020] [Indexed: 01/09/2023] Open
Abstract
The Atacama Desert is the most arid desert on Earth, focus of important research activities related to microbial biodiversity studies. In this context, metabolic characterization of arid soil bacteria is crucial to understand their survival strategies under extreme environmental stress. We investigated whether strain-specific features of two Microbacterium species were involved in the metabolic ability to tolerate/adapt to local variations within an extreme desert environment. Using an integrative systems biology approach we have carried out construction and comparison of genome-scale metabolic models (GEMs) of two Microbacterium sp., CGR1 and CGR2, previously isolated from physicochemically contrasting soil sites in the Atacama Desert. Despite CGR1 and CGR2 belong to different phylogenetic clades, metabolic pathways and attributes are highly conserved in both strains. However, comparison of the GEMs showed significant differences in the connectivity of specific metabolites related to pH tolerance and CO2 production. The latter is most likely required to handle acidic stress through decarboxylation reactions. We observed greater GEM connectivity within Microbacterium sp. CGR1 compared to CGR2, which is correlated with the capacity of CGR1 to tolerate a wider pH tolerance range. Both metabolic models predict the synthesis of pigment metabolites (β-carotene), observation validated by HPLC experiments. Our study provides a valuable resource to further investigate global metabolic adaptations of bacterial species to grow in soils with different abiotic factors within an extreme environment.
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Ahmad KS. Environmental contaminant 2-chloro-N-(2,6-diethylphenyl)-N-(methoxymethyl)acetamide remediation via Xanthomonas axonopodis and Aspergillus niger. ENVIRONMENTAL RESEARCH 2020; 182:109117. [PMID: 31923851 DOI: 10.1016/j.envres.2020.109117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 12/11/2019] [Accepted: 01/02/2020] [Indexed: 06/10/2023]
Abstract
Alachlor, a chloroacetanilide endocrine disruptor herbicide is precarious for humans as well as the environment. Though banned by the European Union and classified as moderately hazardous by WHO, yet it is nevertheless used in several countries posing austere human and environmental health issues. Alachlor attenuation was scrutinized through simulated biodegradation experiments using soil-isolated microbes. Bio-disintegrative assays of pure three fungal and one bacterial strain; Aspergillus flavus (AF), Penicillium chrysogenum (PC), Aspergillus niger (AN) and Xanthomonas axonopodis (XA), respectively were utilized. Initial Alachlor concentration (10 mg/L) was prepared with individual microbial suspension and monitored for 35 d. Alachlor bio-transformation was analyzed quantitatively and qualitatively by gas chromatography mass spectroscopy. XA and AN displayed maximal potential to metabolise the herbicide while forming residues; 1-chloroacetyl, 2,3- dihydro-7 ethylindole, 7 ethylindole, 7-ethyl-3-methyl-2-methoxy-2,3-dihydroindole, N- (2,6-diethylphenyl)-methyleneamine and 7-Ethyl-N-methylindole. Alachlor degradation by AF, PC, AN and XA was found to be 17.1%, 5.5%, 72.6% and 82.1%, respectively, after 35 d. Microbes have displayed cometabolism as the main mechanism for Alachlor degradation. This research can influence imperative and significant environmental friendly bio-remedial strategies for xenobiotic eradication.
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Affiliation(s)
- Khuram Shahzad Ahmad
- Department of Environmental Sciences, Fatima Jinnah Women University, The Mall, 46000, Rawalpindi, Pakistan.
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28
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Zhang QY, Liu CF, Wang Y, Xia ZF, Huang YJ, Luo XX. Streptomyces roseicoloratus sp. nov., isolated from cotton soil. Int J Syst Evol Microbiol 2020; 70:738-743. [DOI: 10.1099/ijsem.0.003804] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Qiao-Yan Zhang
- College of Life Science, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, Alar 843300, PR China
| | - Chao-feng Liu
- College of Life Science, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, Alar 843300, PR China
| | - Yang Wang
- College of Life Science, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, Alar 843300, PR China
| | - Zhan-Feng Xia
- College of Life Science, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, Alar 843300, PR China
| | - Yao-Jie Huang
- College of Life Science, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, Alar 843300, PR China
| | - Xiao-Xia Luo
- College of Life Science, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, Alar 843300, PR China
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29
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Emmett BD, Buckley DH, Drinkwater LE. Plant growth rate and nitrogen uptake shape rhizosphere bacterial community composition and activity in an agricultural field. THE NEW PHYTOLOGIST 2020; 225:960-973. [PMID: 31487394 DOI: 10.1111/nph.16171] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/27/2019] [Indexed: 06/10/2023]
Abstract
Plant-microbial interactions in the rhizosphere are an essential link in soil nitrogen (N) cycling and plant N supply. Plant phenotype and genotype interact with the soil environment to determine rhizosphere community structure and activity. However, the relative contributions of plant identity, phenology and soil resource availability in shaping rhizosphere effects are not well understood. Four summer annuals and a collection of maize hybrids were grown in a common garden experiment conducted at two levels of organic nutrient availability. Plant biomass, N accumulation, rhizosphere bacterial community composition, and rhizosphere potential extracellular enzyme activity were assessed at vegetative, flowering and grain-filling stages of maize. Plant N uptake was strongly coupled with protease activity in the rhizosphere. Temporal trends in rhizosphere community composition varied between plant species. Changes in rhizosphere community composition could be explained by variation in plant growth dynamics. These findings indicate that species-level variation in plant growth dynamics and resource acquisition drive variation in rhizosphere bacterial community composition and activity linked to plant N uptake.
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Affiliation(s)
- Bryan D Emmett
- Horticulture Section, School of Integrative Plant Science, Cornell University, 134A Plant Science Building, Ithaca, NY, 14853, USA
| | - Daniel H Buckley
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, 232 Emerson Hall, Ithaca, NY, 14853, USA
| | - Laurie E Drinkwater
- Horticulture Section, School of Integrative Plant Science, Cornell University, 134A Plant Science Building, Ithaca, NY, 14853, USA
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30
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Chittal V, Gracias M, Anu A, Saha P, Bhaskara Rao KV. Biodecolorization and Biodegradation of Azo Dye Reactive Orange-16 by Marine Nocardiopsis sp. IRANIAN JOURNAL OF BIOTECHNOLOGY 2019; 17:e1551. [PMID: 32195279 PMCID: PMC7080967 DOI: 10.29252/ijb.1551] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Background: Azo dyes are xenobiotic compounds that have bioaccumulated in the environment due to escalated industrial development.
These are hazardous in nature, possessing carcinogenic and mutagenic effects on human beings. Objectives: The perspective of the present study was to isolate and to determine azo dye (Reactive Orange-16) degrading potential of marine actinobacteria
isolated from sediment samples of Port Blair, India. Material and Methods: Actinobacteria with dye decolorization potential were isolated from sea sediment samples. The actinobacterial isolate with the highest dye decolorizing percentage was identified with the help
of phenotypic, biochemical and molecular studies. The different physico-chemical parameters for dye decolorization were also optimized. The nature of decolorization
by the potent isolate was determined with the help of High Performance Liquid chromatography (HPLC) and Fourier Transformed Infrared spectroscopy (FTIR) techniques.
Further the toxicity of RO-16 decolorized products was investigated with the help of phytotoxcity assay. Results: Out of six actinobacterial isolates, VITVAMB 1 possessed the most efficient RO-16 decolorization property. It decolorized 85.6% of RO-16 (250 mg L-1) within 24hrs.
Isolate VITVAMB 1 was identified to be Nocardiopsis sp. Maximum dye decolorization occurred at pH 8, temperature 35°C, 3% salt concentration
and a dye concentration of 50 mg L-1. Conclusions: The nature of decolorization by Nocardiopsis sp. was biodegradation. Additionally, the degraded dye metabolites were found to be
less toxic than pure dye. The high decolorization potential of VITVAMB 1 and the low toxicity of its degradation products make it a prospective
dye removal system. The marine origin of VITVAMB 1 also makes it an attractive source for novel azo dye reducing enzymes.
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Affiliation(s)
- Vaibhavi Chittal
- Biomolecules Laboratory, Technology Tower (TT 635), Vellore Institute of Technology (VIT) University, Vellore- 632014, Tamil Nadu, India
| | - Magaly Gracias
- Biomolecules Laboratory, Technology Tower (TT 635), Vellore Institute of Technology (VIT) University, Vellore- 632014, Tamil Nadu, India
| | - Anagha Anu
- Biomolecules Laboratory, Technology Tower (TT 635), Vellore Institute of Technology (VIT) University, Vellore- 632014, Tamil Nadu, India
| | - Purbasha Saha
- Biomolecules Laboratory, Technology Tower (TT 635), Vellore Institute of Technology (VIT) University, Vellore- 632014, Tamil Nadu, India
| | - K V Bhaskara Rao
- Biomolecules Laboratory, Technology Tower (TT 635), Vellore Institute of Technology (VIT) University, Vellore- 632014, Tamil Nadu, India
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31
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Colin Y, Goberna M, Verdú M, Navarro-Cano JA. Successional trajectories of soil bacterial communities in mine tailings: The role of plant functional traits. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 241:284-292. [PMID: 31009816 DOI: 10.1016/j.jenvman.2019.04.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 02/20/2019] [Accepted: 04/07/2019] [Indexed: 06/09/2023]
Abstract
Plant species identity is assumed to be a major driver of belowground microbial diversity and composition. However, diagnosing which plant functional traits are responsible for shaping microbial communities remains elusive. Primary succession on barren metalliferous mining substrates was selected as the framework to study above-belowground interactions, and plant functional traits that lead the successional trajectories of soil bacterial communities were identified. The impact of the plant functional group (i.e. trees, shrubs, dwarf shrubs, perennial grasses), a trait integrating the life span and morphological structure, on the bacterial primary succession was monitored. Bacterial diversity and composition was estimated along plant size gradients including over 90 scattered patches ranging from seedlings to mature multispecific patches. Soil bacterial diversity was affected by heavy metals levels and increased towards higher resource availability underneath mature patches, with stress-tolerant heterotrophs and phototrophs being replaced by competitive heterotrophs. The plant functional group modulated these general patterns and shrubs had the greatest impact belowground by inducing the largest increase in soil fertility. Functional traits related to leaf decomposability and root architecture further determined the composition and structure of bacterial communities. These results underline the importance of plant functional traits in the assembly of soil bacterial communities, and can help guiding restoration of degraded lands.
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Affiliation(s)
- Yannick Colin
- Centro de Investigaciones sobre Desertificación (CSIC-UVEG-GV), Carretera Moncada ‒ Náquera, km 4.5, Moncada, Valencia, 46113, Spain.
| | - Marta Goberna
- Centro de Investigaciones sobre Desertificación (CSIC-UVEG-GV), Carretera Moncada ‒ Náquera, km 4.5, Moncada, Valencia, 46113, Spain; Department of Environment and Agronomy, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Ctra. de la Coruña, km 7.5, E-28040, Madrid, Spain
| | - Miguel Verdú
- Centro de Investigaciones sobre Desertificación (CSIC-UVEG-GV), Carretera Moncada ‒ Náquera, km 4.5, Moncada, Valencia, 46113, Spain
| | - Jose A Navarro-Cano
- Centro de Investigaciones sobre Desertificación (CSIC-UVEG-GV), Carretera Moncada ‒ Náquera, km 4.5, Moncada, Valencia, 46113, Spain
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32
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Cho MA, Han S, Lim YR, Kim V, Kim H, Kim D. Streptomyces Cytochrome P450 Enzymes and Their Roles in the Biosynthesis of Macrolide Therapeutic Agents. Biomol Ther (Seoul) 2019; 27:127-133. [PMID: 30562877 PMCID: PMC6430224 DOI: 10.4062/biomolther.2018.183] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/08/2018] [Accepted: 10/08/2018] [Indexed: 12/14/2022] Open
Abstract
The study of the genus Streptomyces is of particular interest because it produces a wide array of clinically important bioactive molecules. The genomic sequencing of many Streptomyces species has revealed unusually large numbers of cytochrome P450 genes, which are involved in the biosynthesis of secondary metabolites. Many macrolide biosynthetic pathways are catalyzed by a series of enzymes in gene clusters including polyketide and non-ribosomal peptide synthesis. In general, Streptomyces P450 enzymes accelerate the final, post-polyketide synthesis steps to enhance the structural architecture of macrolide chemistry. In this review, we discuss the major Streptomyces P450 enzymes research focused on the biosynthetic processing of macrolide therapeutic agents, with an emphasis on their biochemical mechanisms and structural insights.
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Affiliation(s)
- Myung-A Cho
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
| | - Songhee Han
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
| | - Young-Ran Lim
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
| | - Vitchan Kim
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
| | - Harim Kim
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
| | - Donghak Kim
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
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33
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Landesman WJ, Freedman ZB, Nelson DM. Seasonal, sub-seasonal and diurnal variation of soil bacterial community composition in a temperate deciduous forest. FEMS Microbiol Ecol 2019; 95:5281420. [PMID: 30629168 PMCID: PMC6353803 DOI: 10.1093/femsec/fiz002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/05/2019] [Indexed: 02/01/2023] Open
Abstract
The temporal dynamics of soil bacterial communities are understudied, but such understanding is critical to elucidating the drivers of community variation. The goal of this study was to characterize how soil bacterial communities vary across diurnal, sub-seasonal and seasonal time-scales in a 5.8 m2 plot and test the hypothesis that bacterial diversity varies on each of these scales. We used 16S rDNA gene amplicon sequencing to quantify the alpha and beta diversity of soil bacteria as well as the Net Relatedness Index and Nearest Taxon Indices to assess the degree of phylogenetic clustering, and the extent to which community shifts were driven by stochastic vs. deterministic limitation. We found that species richness was highest in winter, lowest in fall and that communities were compositionally distinct across seasons. There was no evidence of diurnal-scale shifts; the finest temporal scale over which community shifts were detected using our DNA-based analysis was between sampling dates separated by 6 weeks. Phylogenetic analyses suggested that seasonal-scale differences in community composition were the result of environmental filtering and homogeneous selection. Our findings provide insight into temporal variation of soil bacterial communities across the hourly to seasonal scales while minimizing the potential confounding effect of spatial variation.
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Affiliation(s)
- William J Landesman
- Biology Program, Green Mountain College, One Brennan Circle, Poultney, VT 05764
| | - Zachary B Freedman
- Division of Plant and Soil Sciences, West Virginia University, 370 Evansdale Drive, Morgantown, WV 26506
| | - David M Nelson
- Appalachian Laboratory, University of Maryland Center for Environmental Science, 301 Braddock Road, Frostburg, MD 21532
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34
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Cai L, Gong X, Sun X, Li S, Yu X. Comparison of chemical and microbiological changes during the aerobic composting and vermicomposting of green waste. PLoS One 2018; 13:e0207494. [PMID: 30475832 PMCID: PMC6261053 DOI: 10.1371/journal.pone.0207494] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/30/2018] [Indexed: 01/01/2023] Open
Abstract
This research was conducted to compare chemical and microbiological properties during aerobic composting (AC) and vermicomposting (VC) of green waste. Relative to AC, VC significantly decreased the pH and lignin and cellulose contents, and significantly increased the electrical conductivity and total N and available P contents. For AC, BIrii41_norank (order Myxococcales) was the major bacterial genus at 30 d and again became dominant genus from 90–150 d, with relative abundances of 2.88% and 4.77–5.19%, respectively; at 45 d and 60 d, the dominant bacterial genus was Nitrosomonadaceae_uncultured (order Nitrosomonadales) with relative abundances of 2.83–7.17%. For VC, the dominant bacterial genus was BIrii41_norank (except at 45 d), which accounted for 2.11–7.96% of the total reads. The dominant fungal class was Sordariomycetes in AC (relative abundances 39.2–80.6%) and VC (relative abundances 42.1–69.5%). The abundances of microbial taxa and therefore the bacterial and fungal community structures differed between VC and AC. The quality of the green waste compost product was higher with VC than with AC. These results will also help to achieve further composting technology breakthroughs in reducing the composting time and improving compost quality.
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Affiliation(s)
- Linlin Cai
- College of Forestry, Beijing Forestry University, Beijing, P.R. China
| | - Xiaoqiang Gong
- College of Forestry, Beijing Forestry University, Beijing, P.R. China
| | - Xiangyang Sun
- College of Forestry, Beijing Forestry University, Beijing, P.R. China
| | - Suyan Li
- College of Forestry, Beijing Forestry University, Beijing, P.R. China
| | - Xin Yu
- College of Forestry, Beijing Forestry University, Beijing, P.R. China
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35
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Arancibia NB, Solans M, Mestre MC, Chaia EE. Effect of Pinus ponderosa afforestation on soilborne Frankia and saprophytic Actinobacteria in Northwest Patagonia, Argentina. Symbiosis 2018. [DOI: 10.1007/s13199-018-0538-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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36
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Genderjahn S, Alawi M, Mangelsdorf K, Horn F, Wagner D. Desiccation- and Saline-Tolerant Bacteria and Archaea in Kalahari Pan Sediments. Front Microbiol 2018; 9:2082. [PMID: 30294305 PMCID: PMC6158459 DOI: 10.3389/fmicb.2018.02082] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 08/14/2018] [Indexed: 01/22/2023] Open
Abstract
More than 41% of the Earth's land area is covered by permanent or seasonally arid dryland ecosystems. Global development and human activity have led to an increase in aridity, resulting in ecosystem degradation and desertification around the world. The objective of the present work was to investigate and compare the microbial community structure and geochemical characteristics of two geographically distinct saline pan sediments in the Kalahari Desert of southern Africa. Our data suggest that these microbial communities have been shaped by geochemical drivers, including water content, salinity, and the supply of organic matter. Using Illumina 16S rRNA gene sequencing, this study provides new insights into the diversity of bacteria and archaea in semi-arid, saline, and low-carbon environments. Many of the observed taxa are halophilic and adapted to water-limiting conditions. The analysis reveals a high relative abundance of halophilic archaea (primarily Halobacteria), and the bacterial diversity is marked by an abundance of Gemmatimonadetes and spore-forming Firmicutes. In the deeper, anoxic layers, candidate division MSBL1, and acetogenic bacteria (Acetothermia) are abundant. Together, the taxonomic information and geochemical data suggest that acetogenesis could be a prevalent form of metabolism in the deep layers of a saline pan.
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Affiliation(s)
- Steffi Genderjahn
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Potsdam, Germany.,GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 3.2 Organic Geochemistry, Potsdam, Germany
| | - Mashal Alawi
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Potsdam, Germany
| | - Kai Mangelsdorf
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 3.2 Organic Geochemistry, Potsdam, Germany
| | - Fabian Horn
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Potsdam, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Potsdam, Germany.,Institute of Earth and Environmental Science, University of Potsdam, Potsdam, Germany
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37
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Ren M, Zhang Z, Wang X, Zhou Z, Chen D, Zeng H, Zhao S, Chen L, Hu Y, Zhang C, Liang Y, She Q, Zhang Y, Peng N. Diversity and Contributions to Nitrogen Cycling and Carbon Fixation of Soil Salinity Shaped Microbial Communities in Tarim Basin. Front Microbiol 2018; 9:431. [PMID: 29593680 PMCID: PMC5855357 DOI: 10.3389/fmicb.2018.00431] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 02/26/2018] [Indexed: 11/14/2022] Open
Abstract
Arid and semi-arid regions comprise nearly one-fifth of the earth's terrestrial surface. However, the diversities and functions of their soil microbial communities are not well understood, despite microbial ecological importance in driving biogeochemical cycling. Here, we analyzed the geochemistry and microbial communities of the desert soils from Tarim Basin, northwestern China. Our geochemical data indicated half of these soils are saline. Metagenomic analysis showed that bacterial phylotypes (89.72% on average) dominated the community, with relatively small proportions of Archaea (7.36%) and Eukaryota (2.21%). Proteobacteria, Firmicutes, Actinobacteria, and Euryarchaeota were most abundant based on metagenomic data, whereas genes attributed to Proteobacteria, Actinobacteria, Euryarchaeota, and Thaumarchaeota most actively transcribed. The most abundant phylotypes (Halobacterium, Halomonas, Burkholderia, Lactococcus, Clavibacter, Cellulomonas, Actinomycetospora, Beutenbergia, Pseudomonas, and Marinobacter) in each soil sample, based on metagenomic data, contributed marginally to the population of all microbial communities, whereas the putative halophiles, which contributed the most abundant transcripts, were in the majority of the active microbial population and is consistent with the soil salinity. Sample correlation analyses according to the detected and active genotypes showed significant differences, indicating high diversity of microbial communities among the Tarim soil samples. Regarding ecological functions based on the metatranscriptomic data, transcription of genes involved in various steps of nitrogen cycling, as well as carbon fixation, were observed in the tested soil samples. Metatranscriptomic data also indicated that Thaumarchaeota are crucial for ammonia oxidation and Proteobacteria play the most important role in other steps of nitrogen cycle. The reductive TCA pathway and dicarboxylate-hydroxybutyrate cycle attributed to Proteobacteria and Crenarchaeota, respectively, were highly represented in carbon fixation. Our study reveals that the microbial communities could provide carbon and nitrogen nutrients for higher plants in the sandy saline soils of Tarim Basin.
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Affiliation(s)
- Min Ren
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhufeng Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xuelian Wang
- Center for Genome Analysis, ABLife Inc., Wuhan, China
| | - Zhiwei Zhou
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Dong Chen
- Center for Genome Analysis, ABLife Inc., Wuhan, China
| | - Hui Zeng
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Wuhan, China
| | - Shumiao Zhao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Lingling Chen
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Yuanliang Hu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China.,Hubei Key Laboratory of Edible Wild Plants Conservation & Utilization, College of Life Sciences, Hubei Normal University, Huangshi, China
| | - Changyi Zhang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Yunxiang Liang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qunxin She
- Department of Biology, Archaeal Centre, University of Copenhagen, Copenhagen, Denmark
| | - Yi Zhang
- Center for Genome Analysis, ABLife Inc., Wuhan, China.,Laboratory for Genome Regulation and Human Health, ABLife Inc., Wuhan, China
| | - Nan Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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38
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Emmett BD, Youngblut ND, Buckley DH, Drinkwater LE. Plant Phylogeny and Life History Shape Rhizosphere Bacterial Microbiome of Summer Annuals in an Agricultural Field. Front Microbiol 2017; 8:2414. [PMID: 29321763 PMCID: PMC5732146 DOI: 10.3389/fmicb.2017.02414] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/22/2017] [Indexed: 11/15/2022] Open
Abstract
Rhizosphere microbial communities are critically important for soil nitrogen cycling and plant productivity. There is evidence that plant species and genotypes select distinct rhizosphere communities, however, knowledge of the drivers and extent of this variation remains limited. We grew 11 annual species and 11 maize (Zea mays subsp. mays) inbred lines in a common garden experiment to assess the influence of host phylogeny, growth, and nitrogen metabolism on rhizosphere communities. Growth characteristics, bacterial community composition and potential activity of extracellular enzymes were assayed at time of flowering, when plant nitrogen demand is maximal. Bacterial community composition varied significantly between different plant species and genotypes. Rhizosphere beta-diversity was positively correlated with phylogenetic distance between plant species, but not genetic distance within a plant species. In particular, life history traits associated with plant resource acquisition (e.g., longer lifespan, high nitrogen use efficiency, and larger seed size) were correlated with variation in bacterial community composition and enzyme activity. These results indicate that plant evolutionary history and life history strategy influence rhizosphere bacterial community composition and activity. Thus, incorporating phylogenetic or functional diversity into crop rotations may be a tool to manipulate plant-microbe interactions in agricultural systems.
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Affiliation(s)
- Bryan D. Emmett
- Horticulture Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Nicholas D. Youngblut
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Daniel H. Buckley
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Laurie E. Drinkwater
- Horticulture Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
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39
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Mogul R, Vaishampayan P, Bashir M, McKay CP, Schubert K, Bornaccorsi R, Gomez E, Tharayil S, Payton G, Capra J, Andaya J, Bacon L, Bargoma E, Black D, Boos K, Brant M, Chabot M, Chau D, Cisneros J, Chu G, Curnutt J, DiMizio J, Engelbrecht C, Gott C, Harnoto R, Hovanesian R, Johnson S, Lavergne B, Martinez G, Mans P, Morales E, Oei A, Peplow G, Piaget R, Ponce N, Renteria E, Rodriguez V, Rodriguez J, Santander M, Sarmiento K, Scheppelmann A, Schroter G, Sexton D, Stephenson J, Symer K, Russo-Tait T, Weigel B, Wilhelm MB. Microbial Community and Biochemical Dynamics of Biological Soil Crusts across a Gradient of Surface Coverage in the Central Mojave Desert. Front Microbiol 2017; 8:1974. [PMID: 29109701 PMCID: PMC5660283 DOI: 10.3389/fmicb.2017.01974] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/25/2017] [Indexed: 02/01/2023] Open
Abstract
In this study, we expand upon the biogeography of biological soil crusts (BSCs) and provide molecular insights into the microbial community and biochemical dynamics along the vertical BSC column structure, and across a transect of increasing BSC surface coverage in the central Mojave Desert, CA, United States. Next generation sequencing reveals a bacterial community profile that is distinct among BSCs in the southwestern United States. Distribution of major phyla in the BSC topsoils included Cyanobacteria (33 ± 8%), Proteobacteria (26 ± 6%), and Chloroflexi (12 ± 4%), with Phormidium being the numerically dominant genus. Furthermore, BSC subsurfaces contained Proteobacteria (23 ± 5%), Actinobacteria (20 ± 5%), and Chloroflexi (18 ± 3%), with an unidentified genus from Chloroflexi (AKIW781, order) being numerically dominant. Across the transect, changes in distribution at the phylum (p < 0.0439) and genus (p < 0.006) levels, including multiple biochemical and geochemical trends (p < 0.05), positively correlated with increasing BSC surface coverage. This included increases in (a) Chloroflexi abundance, (b) abundance and diversity of Cyanobacteria, (b) OTU-level diversity in the topsoil, (c) OTU-level differentiation between the topsoil and subsurface, (d) intracellular ATP abundances and catalase activities, and (e) enrichments in clay, silt, and varying elements, including S, Mn, Co, As, and Pb, in the BSC topsoils. In sum, these studies suggest that BSCs from regions of differing surface coverage represent early successional stages, which exhibit increasing bacterial diversity, metabolic activities, and capacity to restructure the soil. Further, these trends suggest that BSC successional maturation and colonization across the transect are inhibited by metals/metalloids such as B, Ca, Ti, Mn, Co, Ni, Mo, and Pb.
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Affiliation(s)
- Rakesh Mogul
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Parag Vaishampayan
- Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Blue Marble Space Institute of Science, Seattle, WA, United States.,Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Mina Bashir
- Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States.,Division of Endocrinology and Diabetology, Medical University of Graz, Graz, Austria
| | - Chris P McKay
- Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Ames Research Center, National Aeronautics and Space Administration, Mountain View, CA, United States
| | - Keith Schubert
- Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Department of Computer Science, Baylor University, Waco, TX, United States
| | - Rosalba Bornaccorsi
- Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States.,SETI Institute, Mountain View, CA, United States
| | - Ernesto Gomez
- Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Department of Computer Science, California State University, San Bernardino, San Bernardino, CA, United States
| | - Sneha Tharayil
- College of Education, University of Texas at Austin, Austin, TX, United States.,Teacher Core, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Geoffrey Payton
- Teacher Core, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Orchard Academies 2B: Arts and Media, Bell, CA, United States
| | - Juliana Capra
- Teacher Core, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Foothills Middle School, Arcadia, CA, United States
| | - Jessica Andaya
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Leonard Bacon
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Maple Hill High School, Castleton-on-Hudson, NY, United States
| | - Emily Bargoma
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - David Black
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,American Academy of Innovation, Jordan, UT, United States
| | - Katie Boos
- College of Education, University of Texas at Austin, Austin, TX, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Michaela Brant
- College of Education, University of Texas at Austin, Austin, TX, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Michael Chabot
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Danny Chau
- Orchard Academies 2B: Arts and Media, Bell, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Jessica Cisneros
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Geoff Chu
- Ames Research Center, National Aeronautics and Space Administration, Mountain View, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Jane Curnutt
- Department of Computer Science, Baylor University, Waco, TX, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Jessica DiMizio
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Excellence in STEM Education, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Christian Engelbrecht
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Math and Science Education, San Francisco State University, San Francisco, CA, United States
| | - Caroline Gott
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Raechel Harnoto
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Excellence in STEM Education, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Ruben Hovanesian
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Shane Johnson
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Excellence in STEM Education, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Britne Lavergne
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Math and Science Education, San Francisco State University, San Francisco, CA, United States
| | - Gabriel Martinez
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Paul Mans
- Ames Research Center, National Aeronautics and Space Administration, Mountain View, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Ernesto Morales
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Alex Oei
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Gary Peplow
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Smiley Elementary School, Redlands, CA, United States
| | - Ryan Piaget
- Ames Research Center, National Aeronautics and Space Administration, Mountain View, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Nicole Ponce
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Math and Science Education, San Francisco State University, San Francisco, CA, United States
| | - Eduardo Renteria
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Veronica Rodriguez
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Joseph Rodriguez
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Monica Santander
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Khamille Sarmiento
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Allison Scheppelmann
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Excellence in STEM Education, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Gavin Schroter
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Excellence in STEM Education, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Devan Sexton
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Jenin Stephenson
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Math and Science Education, San Francisco State University, San Francisco, CA, United States
| | - Kristin Symer
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Excellence in STEM Education, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Tatiane Russo-Tait
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Math and Science Education, San Francisco State University, San Francisco, CA, United States
| | - Bill Weigel
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Mary B Wilhelm
- Ames Research Center, National Aeronautics and Space Administration, Mountain View, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
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40
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Kizito S, Lv T, Wu S, Ajmal Z, Luo H, Dong R. Treatment of anaerobic digested effluent in biochar-packed vertical flow constructed wetland columns: Role of media and tidal operation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 592:197-205. [PMID: 28319707 DOI: 10.1016/j.scitotenv.2017.03.125] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/12/2017] [Accepted: 03/12/2017] [Indexed: 05/22/2023]
Abstract
Three types of vertical flow constructed wetland columns (VFCWs), packed with corn cob biochar (CB-CW), wood biochar (WB-CW) and gravel (G-CW) under tidal flow operations, were comparatively evaluated to investigate anaerobic digested effluent treatment performance and mechanisms. It was demonstrated that CB-CW and WB-CW provide significantly higher removal efficiencies for organic matter (>59%), NH4+-N (>76%), TN (>37%) and phosphorus (>71%), compared with G-CW (22%-49%). The higher pollutants removal ability of biochar-packed VFCWs was mainly attribute to the higher adsorption ability and microbial cultivation in the porous biochar media. Moreover, increasing the flooded/drained ratio from 4/8h to 8/4h of the tidal operation further improved around 10% of the removal of both organics and NH4+-N for biochar-packed VFCWs. The phosphorus removal was dependent on the media adsorption capacities through the whole experiment. However, the NH4+-N biodegradation by microbial communities was demonstrated to become the dominant removal mechanism in the long term treatment, which compensated the decreased adsorption capacities of the media. The study supported that the use of biochar would increase the treatment performance and elongate the lifespan of CWs under tidal operation.
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Affiliation(s)
- Simon Kizito
- Key Laboratory of Clean Utilization Technology for Renewable Energy, Ministry of Agriculture, College of Engineering, China Agricultural University, 100083 Beijing, PR China; College of Agriculture and Environmental Sciences, Makerere University, 7062 Kampala, Uganda
| | - Tao Lv
- Department of Bioscience, Aarhus University, Aarhus 8000C, Denmark
| | - Shubiao Wu
- Key Laboratory of Clean Utilization Technology for Renewable Energy, Ministry of Agriculture, College of Engineering, China Agricultural University, 100083 Beijing, PR China.
| | - Zeeshan Ajmal
- Key Laboratory of Clean Utilization Technology for Renewable Energy, Ministry of Agriculture, College of Engineering, China Agricultural University, 100083 Beijing, PR China
| | - Hongzhen Luo
- Key Laboratory of Clean Utilization Technology for Renewable Energy, Ministry of Agriculture, College of Engineering, China Agricultural University, 100083 Beijing, PR China
| | - Renjie Dong
- Key Laboratory of Clean Utilization Technology for Renewable Energy, Ministry of Agriculture, College of Engineering, China Agricultural University, 100083 Beijing, PR China
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41
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Lewin GR, Carlos C, Chevrette MG, Horn HA, McDonald BR, Stankey RJ, Fox BG, Currie CR. Evolution and Ecology of Actinobacteria and Their Bioenergy Applications. Annu Rev Microbiol 2017; 70:235-54. [PMID: 27607553 DOI: 10.1146/annurev-micro-102215-095748] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ancient phylum Actinobacteria is composed of phylogenetically and physiologically diverse bacteria that help Earth's ecosystems function. As free-living organisms and symbionts of herbivorous animals, Actinobacteria contribute to the global carbon cycle through the breakdown of plant biomass. In addition, they mediate community dynamics as producers of small molecules with diverse biological activities. Together, the evolution of high cellulolytic ability and diverse chemistry, shaped by their ecological roles in nature, make Actinobacteria a promising group for the bioenergy industry. Specifically, their enzymes can contribute to industrial-scale breakdown of cellulosic plant biomass into simple sugars that can then be converted into biofuels. Furthermore, harnessing their ability to biosynthesize a range of small molecules has potential for the production of specialty biofuels.
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Affiliation(s)
- Gina R Lewin
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Camila Carlos
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Marc G Chevrette
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Heidi A Horn
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706;
| | - Bradon R McDonald
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Robert J Stankey
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Brian G Fox
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726.,Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
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42
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Frasch HJ, Leeuwen SSV, Dijkhuizen L. Molecular and biochemical characteristics of the inulosucrase HugO from Streptomyces viridochromogenes DSM40736 (Tü494). Microbiology (Reading) 2017; 163:1030-1041. [DOI: 10.1099/mic.0.000493] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Hans-Jörg Frasch
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Sander S. van Leeuwen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Lubbert Dijkhuizen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
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43
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Das S, Chou ML, Jean JS, Yang HJ, Kim PJ. Arsenic-enrichment enhanced root exudates and altered rhizosphere microbial communities and activities in hyperaccumulator Pteris vittata. JOURNAL OF HAZARDOUS MATERIALS 2017; 325:279-287. [PMID: 27940117 DOI: 10.1016/j.jhazmat.2016.12.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 12/01/2016] [Accepted: 12/02/2016] [Indexed: 06/06/2023]
Abstract
Phytoremediation of arsenic (As)-contaminated soil by hyperaccumulator Pteris vittata is promising. A better understanding of the rhizosphere microbial dynamics that regulate As availability and plant growth is important to optimize the phytoremediation process. In this study, Illumina sequencing of 16S rRNA genes was applied to assess the rhizosphere microbial community structure of P. vittata. Microbial functionality was monitored by soil enzyme activities and MPN-PCR targeting genes of interest. Arsenic (100mgkg-1 AsV) addition to soil significantly increased DOC, root exudates, As and P uptake and the frond biomass of P. vittata. Moreover, As-enrichment significantly increased soil enzyme activities involved in N, P and S cycling and the gene abundance of As transforming bacteria, Fe- and S-reducing bacteria and N and C fixing bacteria in the rhizosphere of P. vittata. Together, the results revealed that the combined selective pressure of As and rhizosphere resulted in stimulation of microbial community, which most likely has a role in reductive dissolution of Fe and S, As and P mobilization, C degradation and fixation, and N fixation. These changes appeared to have a role in mitigation of As toxicity and to promote growth and the As uptake ability of P. vittata under As-enriched conditions.
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Affiliation(s)
- Suvendu Das
- Department of Earth Sciences, National Cheng Kung University, Tainan 70101, Taiwan; Institute of Agricultural Science and Life Science, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Mon-Lin Chou
- Department of Earth Sciences, National Cheng Kung University, Tainan 70101, Taiwan
| | - Jiin-Shuh Jean
- Department of Earth Sciences, National Cheng Kung University, Tainan 70101, Taiwan.
| | - Huai-Jen Yang
- Department of Earth Sciences, National Cheng Kung University, Tainan 70101, Taiwan
| | - Pil Joo Kim
- Institute of Agricultural Science and Life Science, Gyeongsang National University, Jinju 660-701, Republic of Korea
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44
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Soil microorganisms can overcome respiration inhibition by coupling intra- and extracellular metabolism: 13C metabolic tracing reveals the mechanisms. ISME JOURNAL 2017; 11:1423-1433. [PMID: 28157187 DOI: 10.1038/ismej.2017.3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 11/24/2016] [Accepted: 01/04/2017] [Indexed: 11/08/2022]
Abstract
CO2 release from soil is commonly used to estimate toxicity of various substances on microorganisms. However, the mechanisms underlying persistent CO2 release from soil exposed to toxicants inhibiting microbial respiration, for example, sodium azide (NaN3) or heavy metals (Cd, Hg, Cu), remain unclear. To unravel these mechanisms, NaN3-amended soil was incubated with position-specifically 13C-labeled glucose and 13C was quantified in CO2, bulk soil, microbial biomass and phospholipid fatty acids (PLFAs). High 13C recovery from C-1 in CO2 indicates that glucose was predominantly metabolized via the pentose phosphate pathway irrespective of inhibition. Although NaN3 prevented 13C incorporation into PLFA and decreased total CO2 release, 13C in CO2 increased by 12% compared with control soils due to an increased use of glucose for energy production. The allocation of glucose-derived carbon towards extracellular compounds, demonstrated by a fivefold higher 13C recovery in bulk soil than in microbial biomass, suggests the synthesis of redox active substances for extracellular disposal of electrons to bypass inhibited electron transport chains within the cells. PLFA content doubled within 10 days of inhibition, demonstrating recovery of the microbial community. This growth was largely based on recycling of cost-intensive biomass compounds, for example, alkyl chains, from microbial necromass. The bypass of intracellular toxicity by extracellular electron transport permits the fast recovery of the microbial community. Such efficient strategies to overcome exposure to respiration-inhibiting toxicants may be exclusive to habitats containing redox-sensitive substances. Therefore, the toxic effects of respiration inhibitors on microorganisms are much less intensive in soils than in pure cultures.
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Suriya J, Bharathiraja S, Manivasagan P, Kim SK. Enzymes From Rare Actinobacterial Strains. ADVANCES IN FOOD AND NUTRITION RESEARCH 2016; 79:67-98. [PMID: 27770864 DOI: 10.1016/bs.afnr.2016.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Actinobacteria constitute rich sources of novel biocatalysts and novel natural products for medical and industrial utilization. Although actinobacteria are potential source of economically important enzymes, the isolation and culturing are somewhat tough because of its extreme habitats. But now-a-days, the rate of discovery of novel compounds producing actinomycetes from soil, freshwater, and marine ecosystem has increased much through the developed culturing and genetic engineering techniques. Actinobacteria are well-known source of their bioactive compounds and they are the promising source of broad range of industrially important enzymes. The bacteria have the capability to degrade a range of pesticides, hydrocarbons, aromatic, and aliphatic compounds (Sambasiva Rao, Tripathy, Mahalaxmi, & Prakasham, 2012). Most of the enzymes are mainly derived from microorganisms because of their easy of growth, minimal nutritional requirements, and low-cost for downstream processing. The focus of this review is about the new, commercially useful enzymes from rare actinobacterial strains. Industrial requirements are now fulfilled by the novel actinobacterial enzymes which assist the effective production. Oxidative enzymes, lignocellulolytic enzymes, extremozymes, and clinically useful enzymes are often utilized in many industrial processes because of their ability to catalyze numerous reactions. Novel, extremophilic, oxidative, lignocellulolytic, and industrially important enzymes from rare Actinobacterial population are discussed in this chapter.
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Affiliation(s)
- J Suriya
- School of Environmental Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - S Bharathiraja
- CAS in Marine Biology, Annamalai University, Porto Novo, Tamil Nadu, India
| | - P Manivasagan
- Marine Bioprocess Research Center, Pukyong National University, Busan, Republic of Korea.
| | - S-K Kim
- Marine Bioprocess Research Center, Pukyong National University, Busan, Republic of Korea; Specialized Graduate School Science & Technology Convergence, Pukyong National University, Busan, Republic of Korea.
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Jensen PR. Natural Products and the Gene Cluster Revolution. Trends Microbiol 2016; 24:968-977. [PMID: 27491886 DOI: 10.1016/j.tim.2016.07.006] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/29/2016] [Accepted: 07/19/2016] [Indexed: 11/24/2022]
Abstract
Genome sequencing has created unprecedented opportunities for natural-product discovery and new insight into the diversity and distributions of natural-product biosynthetic gene clusters (BGCs). These gene collectives are highly evolved for horizontal exchange, thus providing immediate opportunities to test the effects of small molecules on fitness. The marine actinomycete genus Salinispora maintains extraordinary levels of BGC diversity and has become a useful model for studies of secondary metabolism. Most Salinispora BGCs are observed infrequently, resulting in high population-level diversity while conforming to constraints associated with maximum genome size. Comparative genomics is providing a mechanism to assess secondary metabolism in the context of evolution and evidence that some products represent ecotype-defining traits while others appear selectively neutral.
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Affiliation(s)
- Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Center for Microbiome Innovation, Scripps Institution of Oceanography, University of California San Diego, San Diego, California, USA.
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Choudoir MJ, Doroghazi JR, Buckley DH. Latitude delineates patterns of biogeography in terrestrial Streptomyces. Environ Microbiol 2016; 18:4931-4945. [PMID: 27322415 DOI: 10.1111/1462-2920.13420] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/04/2016] [Indexed: 01/23/2023]
Abstract
The biogeography of Streptomyces was examined at regional spatial scales to identify factors that govern patterns of microbial diversity. Streptomyces are spore forming filamentous bacteria which are widespread in soil. Streptomyces strains were isolated from perennial grass habitats sampled across a spatial scale of more than 6000 km. Previous analysis of this geographically explicit culture collection provided evidence for a latitudinal diversity gradient in Streptomyces species. Here the hypothesis that this latitudinal diversity gradient is a result of evolutionary dynamics associated with historical demographic processes was evaluated. Historical demographic phenomena have genetic consequences that can be evaluated through analysis of population genetics. Population genetic approaches were applied to analyze population structure in six of the most numerically abundant and geographically widespread Streptomyces phylogroups from our culture collection. Streptomyces population structure varied at regional spatial scales, and allelic diversity correlated with geographic distance. In addition, allelic diversity and gene flow are partitioned by latitude. Finally, it was found that nucleotide diversity within phylogroups was negatively correlated with latitude. These results indicate that phylogroup diversification is constrained by dispersal limitation at regional spatial scales, and they are consistent with the hypothesis that historical demographic processes have influenced the contemporary biogeography of Streptomyces.
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Affiliation(s)
- Mallory J Choudoir
- School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - James R Doroghazi
- School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Daniel H Buckley
- School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
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Chaplin AK, Wilson MT, Hough MA, Svistunenko DA, Hemsworth GR, Walton PH, Vijgenboom E, Worrall JAR. Heterogeneity in the Histidine-brace Copper Coordination Sphere in Auxiliary Activity Family 10 (AA10) Lytic Polysaccharide Monooxygenases. J Biol Chem 2016; 291:12838-12850. [PMID: 27129229 DOI: 10.1074/jbc.m116.722447] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Indexed: 12/23/2022] Open
Abstract
Copper-dependent lytic polysaccharide monooxygenases (LPMOs) are enzymes that oxidatively deconstruct polysaccharides. The active site copper in LPMOs is coordinated by a histidine-brace. This utilizes the amino group and side chain of the N-terminal His residue with the side chain of a second His residue to create a T-shaped arrangement of nitrogen ligands. We report a structural, kinetic, and thermodynamic appraisal of copper binding to the histidine-brace in an auxiliary activity family 10 (AA10) LPMO from Streptomyces lividans (SliLPMO10E). Unexpectedly, we discovered the existence of two apo-SliLPMO10E species in solution that can each bind copper at a single site with distinct kinetic and thermodynamic (exothermic and endothermic) properties. The experimental EPR spectrum of copper-bound SliLPMO10E requires the simulation of two different line shapes, implying two different copper-bound species, indicative of three and two nitrogen ligands coordinating the copper. Amino group coordination was probed through the creation of an N-terminal extension variant (SliLPMO10E-Ext). The kinetics and thermodynamics of copper binding to SliLPMO10E-Ext are in accord with copper binding to one of the apo-forms in the wild-type protein, suggesting that amino group coordination is absent in the two-nitrogen coordinate form of SliLPMO10E. Copper binding to SliLPMO10B was also investigated, and again it revealed the presence of two apo-forms with kinetics and stoichiometry of copper binding identical to that of SliLPMO10E. Our findings highlight that heterogeneity exists in the active site copper coordination sphere of LPMOs that may have implications for the mechanism of loading copper in the cell.
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Affiliation(s)
- Amanda K Chaplin
- From the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Michael T Wilson
- From the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Michael A Hough
- From the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Dimitri A Svistunenko
- From the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Glyn R Hemsworth
- the Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom, and
| | - Paul H Walton
- the Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom, and
| | - Erik Vijgenboom
- the Molecular Biotechnology, Institute of Biology, Sylvius Laboratory, Leiden University, P. O. Box 9505, 2300RA Leiden, The Netherlands
| | - Jonathan A R Worrall
- From the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom,.
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Luo X, Sun Y, Xie S, Wan C, Zhang L. Streptomyces indoligenes sp. nov., isolated from rhizosphere soil of Populus euphratica. Int J Syst Evol Microbiol 2016; 66:2424-2428. [PMID: 27031169 DOI: 10.1099/ijsem.0.001049] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinobacterium, designated TRM 43006T, was isolated from the rhizosphere soil of Populus euphratica in Xinjiang Province, north-west China. Phylogenetic and phenotypic analysis demonstrated that strain TRM 43006T belongs to the genus Streptomyces. The strain was aerobic and Gram-stain-positive; the aerial mycelium branched monopodially, forming chains of arthrospores. The spores were oval to cylindrical with smooth surfaces. The whole-cell sugar pattern of strain TRM 43006T consisted of xylose, mannitol, galactose and ribose. The menaquinones were MK-9(H6), MK-9(H8) and MK-9(H10). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol mannosides and four unknown phospholipids. Major fatty acids were iso-C16 : 0, iso-C16 : 1, iso-C14 : 0 and anteiso-C15 : 0. The G+C content of the genomic DNA was 69.0 mol%. Comparative 16S rRNA gene sequence analysis indicated that strain TRM 43006T was phylogenetically most closely related to Streptomyces roseolilacinus NBRC 12815T (98.6 % similarity) and Streptomycessudanensis SD 504T (98.3 %); however, DNA-DNA hybridization studies between S. roseolilacinus NBRC 12815T, S. sudanensis SD 504T and TRM 43006T showed only 30.28 and 30.65 % relatedness, respectively. Based on the evidence from this polyphasic study, strain TRM 43006T represents a novel species of the genus Streptomyces, for which the name Streptomyces indoligenes sp. nov. is proposed. The type strain is TRM 43006T (=KCTC 39611T=CCTCC AA 2015010T).
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Affiliation(s)
- Xiaoxia Luo
- Key Laboratory of Protection and Utilization of Biological Resoures in Tarim Basin of Xinjiang Production & Construction Corps/College of Life Science, Tarim University, Alar 843300, China
| | - Yong Sun
- Key Laboratory of Protection and Utilization of Biological Resoures in Tarim Basin of Xinjiang Production & Construction Corps/College of Life Science, Tarim University, Alar 843300, China
| | - Sinan Xie
- Key Laboratory of Protection and Utilization of Biological Resoures in Tarim Basin of Xinjiang Production & Construction Corps/College of Life Science, Tarim University, Alar 843300, China
| | - Chuanxing Wan
- Key Laboratory of Protection and Utilization of Biological Resoures in Tarim Basin of Xinjiang Production & Construction Corps/College of Life Science, Tarim University, Alar 843300, China
| | - Lili Zhang
- Key Laboratory of Protection and Utilization of Biological Resoures in Tarim Basin of Xinjiang Production & Construction Corps/College of Life Science, Tarim University, Alar 843300, China
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Torondel B, Ensink JHJ, Gundogdu O, Ijaz UZ, Parkhill J, Abdelahi F, Nguyen VA, Sudgen S, Gibson W, Walker AW, Quince C. Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines. Microb Biotechnol 2016; 9:209-23. [PMID: 26875588 PMCID: PMC4767293 DOI: 10.1111/1751-7915.12334] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 10/02/2015] [Accepted: 10/12/2015] [Indexed: 12/15/2022] Open
Abstract
Improving the rate and extent of faecal decomposition in basic forms of sanitation such as pit latrines would benefit around 1.7 billion users worldwide, but to do so requires a major advance in our understanding of the biology of these systems. As a critical first step, bacterial diversity and composition was studied in 30 latrines in Tanzania and Vietnam using pyrosequencing of 16S rRNA genes, and correlated with a number of intrinsic environmental factors such as pH, temperature, organic matter content/composition and geographical factors. Clear differences were observed at the operational taxonomic unit, family and phylum level in terms of richness and community composition between latrines in Tanzania and Vietnam. The results also clearly show that environmental variables, particularly substrate type and availability, can exert a strong structuring influence on bacterial communities in latrines from both countries. The origins and significance of these environmental differences are discussed. This work describes the bacterial ecology of pit latrines in combination with inherent latrine characteristics at an unprecedented level of detail. As such, it provides useful baseline information for future studies that aim to understand the factors that affect decomposition rates in pit latrines.
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Affiliation(s)
- Belen Torondel
- Environmental Health Group, Department of Disease Control, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Jeroen H J Ensink
- Environmental Health Group, Department of Disease Control, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Ozan Gundogdu
- Pathogen Molecular Biology Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | | | - Julian Parkhill
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Faraji Abdelahi
- Ifakara Health Institute, off Mlabani Passage, P.O. Box 53, Ifakara, Tanzania
| | - Viet-Anh Nguyen
- Hanoi University of Civil Engineering, 55 Giai Phong Road, Hanoi, Vietnam
| | - Steven Sudgen
- Environmental Health Group, Department of Disease Control, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Walter Gibson
- Bear Valley Ventures, Braeside, Utkinton Lane, Cotebrook, Tarporley, Cheshire CW6 0JH, UK
| | - Alan W Walker
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK.,Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, AB21 9SB, UK
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