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Matthews K, Cavagnaro T, Weinstein P, Stanhope J. Health by design; optimising our urban environmental microbiomes for human health. ENVIRONMENTAL RESEARCH 2024; 257:119226. [PMID: 38797467 DOI: 10.1016/j.envres.2024.119226] [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: 01/22/2024] [Revised: 05/13/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024]
Abstract
Humans have evolved in direct and intimate contact with their environment and the microbes that it contains, over a period of 2 million years. As a result, human physiology has become intrinsically linked to environmental microbiota. Urbanisation has reduced our exposure to harmful pathogens, however there is now increasing evidence that these same health-protective improvements in our environment may also be contributing to a hidden disease burden: immune dysregulation. Thoughtful and purposeful design has the potential to ameliorate these health concerns by providing sources of microbial diversity for human exposure. In this narrative review, we highlight the role of environmental microbiota in human health and provide insights into how we can optimise human health through well-designed cities, urban landscapes and buildings. The World Health Organization recommends there should be at least one public green space of least 0.5 ha in size within 300m of a place of residence. We argue that these larger green spaces are more likely to permit functioning ecosystems that deliver ecosystem services, including the provision of diverse aerobiomes. Urban planning must consider the conservation and addition of large public green spaces, while landscape design needs to consider how to maximise environmental, social and public health outcomes, which may include rewilding. Landscape designers need to consider how people use these spaces, and how to optimise utilisation, including for those who may experience challenges in access (e.g. those living with disabilities, people in residential care). There are also opportunities to improve health via building design that improves access to diverse environmental microbiota. Considerations include having windows that open, indoor plants, and the relationship between function, form and organization. We emphasise possibilities for re-introducing potentially health-giving microbial exposures into urban environments, particularly where the benefits of exposure to biodiverse environments may have been lost.
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Affiliation(s)
- Kate Matthews
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia; School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
| | - Timothy Cavagnaro
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia; School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia; Environment Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Philip Weinstein
- Environment Institute, The University of Adelaide, Adelaide, SA, Australia; School of Public Health, The University of Adelaide, Adelaide, SA, Australia; South Australian Museum, Adelaide, SA, Australia
| | - Jessica Stanhope
- Environment Institute, The University of Adelaide, Adelaide, SA, Australia; School of Allied Health Science and Practice, The University of Adelaide, Adelaide, SA, Australia.
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Wang S, Zhang Z, Yang K, Zhao J, Zhang W, Wang Z, Liang Z, Zhang Y, Zhang Y, Liu J, Zhang L. SMMP: A Deep-Coverage Marine Metaproteome Method for Microbial Community Analysis throughout the Water Column Using 1 L of Seawater. Anal Chem 2024; 96:12030-12039. [PMID: 39001809 DOI: 10.1021/acs.analchem.4c02079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2024]
Abstract
Marine microbes drive pivotal transformations in planetary-scale elemental cycles and have crucial impacts on global biogeochemical processes. Metaproteomics is a powerful tool for assessing the metabolic diversity and function of marine microbes. However, hundreds of liters of seawater are required for normal metaproteomic analysis due to the sparsity of microbial populations in seawater, which poses a substantial challenge to the widespread application of marine metaproteomics, particularly for deep seawater. Herein, a sensitive marine metaproteomics workflow, named sensitive marine metaproteome analysis (SMMP), was developed by integrating polycarbonate filter-assisted microbial enrichment, solid-phase alkylation-based anti-interference sample preparation, and narrow-bore nanoLC column for trace peptide separation and characterization. The method provided more than 8500 proteins from 1 L of bathypelagic seawater samples, which covered diverse microorganisms and crucial functions, e.g., the detection of key enzymes associated with the Wood-Ljungdahl pathway. Then, we applied SMMP to investigate vertical variations in the metabolic expression patterns of marine microorganisms from the euphotic zone to the bathypelagic zone. Methane oxidation and carbon monoxide (CO) oxidation were active processes, especially in the bathypelagic zone, which provided a remarkable energy supply for the growth and proliferation of heterotrophic microorganisms. In addition, marker protein profiles detected related to ammonia transport, ammonia oxidation, and carbon fixation highlighted that Thaumarchaeota played a critical role in primary production based on the coupled carbon-nitrogen process, contributing to the storage of carbon and nitrogen in the bathypelagic regions. SMMP has low microbial input requirements and yields in-depth metaproteome analysis, making it a prospective approach for comprehensive marine metaproteomic investigations.
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Affiliation(s)
- Songduo Wang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zenghu Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China
- Qingdao New Energy Shandong Laboratory, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Kaiguang Yang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiulong Zhao
- Qingdao New Energy Shandong Laboratory, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Weijie Zhang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiting Wang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Liang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongyu Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China
- Qingdao New Energy Shandong Laboratory, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Yukui Zhang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianhui Liu
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lihua Zhang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Müller A, Stark M, Schottenhammel S, John U, Chacón J, Klingl A, Holzer VJC, Schöffer M, Gottschling M. The second most abundant dinophyte in the ponds of a botanical garden is a species new to science. J Eukaryot Microbiol 2024; 71:e13015. [PMID: 38078515 DOI: 10.1111/jeu.13015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/20/2023] [Accepted: 11/14/2023] [Indexed: 03/10/2024]
Abstract
In the microscopy realm, a large body of dark biodiversity still awaits to be uncovered. Unarmoured dinophytes are particularly neglected here, as they only present inconspicuous traits. In a remote German locality, we collected cells, from which a monoclonal strain was established, to study morphology using light and electron microscopy and to gain DNA sequences from the rRNA operon. In parallel, we detected unicellular eukaryotes in ponds of the Botanical Garden Munich-Nymphenburg by DNA-metabarcoding (V4 region of the 18S rRNA gene), weekly sampled over the course of a year. Strain GeoK*077 turned out to be a new species of Borghiella with a distinct position in molecular phylogenetics and characteristic coccoid cells of ovoid shape as the most important diagnostic trait. Borghiella ovum, sp. nov., was also present in artificial ponds of the Botanical Garden and was the second most abundant dinophyte detected in the samples. More specifically, Borghiella ovum, sp. nov., shows a clear seasonality, with high frequency during winter months and complete absence during summer months. The study underlines the necessity to assess the biodiversity, particularly of the microscopy realm more ambitiously, if even common species such as formerly Borghiella ovum are yet unknown to science.
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Affiliation(s)
- Anna Müller
- Faculty of Biology-Systematics, Biodiversity and Evolution of Plants, GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Marina Stark
- Faculty of Biology-Systematics, Biodiversity and Evolution of Plants, GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sophia Schottenhammel
- Faculty of Biology-Systematics, Biodiversity and Evolution of Plants, GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Uwe John
- Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany
| | - Juliana Chacón
- Faculty of Biology-Systematics, Biodiversity and Evolution of Plants, GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Andreas Klingl
- Faculty of Biology-Plant Development and Electron Microscopy, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Victoria Julia Christine Holzer
- Faculty of Biology-Systematics, Biodiversity and Evolution of Plants, GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Marika Schöffer
- Faculty of Biology-Systematics, Biodiversity and Evolution of Plants, GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Marc Gottschling
- Faculty of Biology-Systematics, Biodiversity and Evolution of Plants, GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
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Kachor A, Tistechok S, Rebets Y, Fedorenko V, Gromyko O. Bacterial community and culturable actinomycetes of Phyllostachys viridiglaucescens rhizosphere. Antonie Van Leeuwenhoek 2024; 117:9. [PMID: 38170239 DOI: 10.1007/s10482-023-01906-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 11/02/2023] [Indexed: 01/05/2024]
Abstract
During the course of development plants form tight interactions with microorganisms inhabiting their root zone. In turn, rhizosphere bacteria, in particular members of the phylum Actinomycetota, positively influence the host plant by increasing access to essential nutrients and controlling the pathogenic microorganism's population. Herein, we report the characterisation of the rhizosphere associated actinobacteria community of Phyllostachys viridiglaucescens growing in the Nikitsky Botanical Garden (Crimean Peninsula, Ukraine). The overall composition of the bacterial community was elucidated by 16S rRNA gene amplicon sequencing followed by isolation of culturable microorganisms with the focus on actinomycetes. The metagenomic approach revealed that the representatives of phylum Actinomycetota (57.1%), Pseudomonadota (20.0%), and Acidobacteriota (12.2%) were dominating in the studied microbiome with Ilumatobacter (phylum Actinomycetota) (13.1%) being the dominant genus. Furthermore, a total of 159 actinomycete isolates, belonging to eight genera of Streptomyces, Micromonospora, Nonomuraea, Arthrobacter, Actinomadura, Kribbella, Cellulosimicrobium, and Mumia, were recovered from P. viridiglaucescens rhizosphere. The isolated species were tested for antimicrobial activity. 64% of isolates were active against at least one bacterial test-culture and 7.5% against fungal test culture. In overall, the rhizosphere bacterial communities act as a great source of actinobacterial diversity with the high potential for production of new bioactive compounds.
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Affiliation(s)
- Anna Kachor
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine
- Explogen LLC, Lviv, 79005, Ukraine
| | - Stepan Tistechok
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine
| | | | - Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine
| | - Oleksandr Gromyko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine.
- Microbial Culture Collection of Antibiotic Producers, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine.
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5
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Calvert J, McTaggart A, Carvalhais LC, Rensink S, Dennis PG, Drenth A, Shivas R. Divergent rainforest tree microbiomes between phases of the monsoon cycle, host plants and tissues. PLANT BIOLOGY (STUTTGART, GERMANY) 2023; 25:860-870. [PMID: 37647418 DOI: 10.1111/plb.13569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 07/26/2023] [Indexed: 09/01/2023]
Abstract
The Australian Monsoon Tropics (AMT) contain some of the most biodiverse forests on the continent. Little is known about the dynamics of rainforest plant microbiomes in general, and there have been no community-level studies on Australian rainforest endophytes, their seasonality, tissue and host specificity. We tested whether community composition of tropical tree endophytes (fungi and bacteria) differs: (i) at different points during a monsoon cycle, (ii) between leaf and stem tissues, (iii) between forest microclimates (gully/ridge), and between (iv) host plant species, and (v) host plant clade, using amplicon sequencing of the bacterial 16S and fungal ITS2 gene regions. Results indicated that the composition of rainforest plant microbiomes differs between wet and dry seasons, which may be explained by physiological shifts in host plants due to annual climate fluctuations from mesic to xeric. Endophyte microbiomes differed between leaves and stems. Distinct fungal communities were associated with host species and clades, with some trees enriched in a number of fungal taxa compared to host plants in other clades. Diversity of bacterial endophytes in plant stems increased in the dry season. We conclude that the microbiomes of tropical plants are responsive to monsoonal climate variation, are highly compartmentalised between plant tissues, and may be partly shaped by the relatedness of their host plants.
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Affiliation(s)
- J Calvert
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Dutton Park, QLD, Australia
| | - A McTaggart
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Dutton Park, QLD, Australia
| | - L C Carvalhais
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Dutton Park, QLD, Australia
| | - S Rensink
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Dutton Park, QLD, Australia
| | - P G Dennis
- School of Earth and Environmental Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - A Drenth
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Dutton Park, QLD, Australia
| | - R Shivas
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Dutton Park, QLD, Australia
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Nisar MA, Ross KE, Brown MH, Bentham R, Xi J, Hinds J, Jamieson T, Leterme SC, Whiley H. The composition of planktonic prokaryotic communities in a hospital building water system depends on both incoming water and flow dynamics. WATER RESEARCH 2023; 243:120363. [PMID: 37494744 DOI: 10.1016/j.watres.2023.120363] [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: 03/23/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/28/2023]
Abstract
In recent years, the frequency of nosocomial infections has increased. Hospital water systems support the growth of microbes, especially opportunistic premise plumbing pathogens. In this study, planktonic prokaryotic communities present in water samples taken from hospital showers and hand basins, collected over three different sampling phases, were characterized by 16S rRNA gene amplicon sequencing. Significant differences in the abundance of various prokaryotic taxa were found through univariate and multivariate analysis. Overall, the prokaryotic communities of hospital water were taxonomically diverse and dominated by biofilm forming, corrosion causing, and potentially pathogenic bacteria. The phyla Proteobacteria, Actinobacteriota, Bacteroidota, Planctomycetota, Firmicutes, and Cyanobacteria made up 96% of the relative abundance. The α-diversity measurements of prokaryotic communities showed no difference in taxa evenness and richness based on sampling sites (shower or hand basins), sampling phases (months), and presence or absence of Vermamoeba vermiformis. However, β-diversity measurements showed significant clustering of prokaryotic communities based on sampling phases, with the greatest difference observed between the samples collected in phase 1 vs phase 2/3. Importantly, significant difference was observed in prokaryotic communities based on flow dynamics of the incoming water. The Pielou's evenness diversity index revealed a significant difference (Kruskal Wallis, p < 0.05) and showed higher species richness in low flow regime (< 13 minutes water flushing per week and ≤ 765 flushing events per six months). Similarly, Bray-Curtis dissimilarity index found significant differences (PERMANOVA, p < 0.05) in the prokaryotic communities of low vs medium/high flow regimes. Furthermore, linear discriminant analysis effect size showed that several biofilm forming (e.g., Pseudomonadales), corrosion causing (e.g., Desulfobacterales), extremely environmental stress resistant (e.g., Deinococcales), and potentially pathogenic (e.g., Pseudomonas) bacterial taxa were in higher amounts under low flow regime conditions. This study demonstrated that a hospital building water system consists of a complex microbiome that is shaped by incoming water quality and the building flow dynamics arising through usage.
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Affiliation(s)
- Muhammad Atif Nisar
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Kirstin E Ross
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Melissa H Brown
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia; ARC Training Centre for Biofilm Research and Innovation, Flinders University, Bedford Park, SA, Australia
| | - Richard Bentham
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - James Xi
- Enware Australia Pty Ltd, Caringbah, NSW, Australia
| | - Jason Hinds
- Enware Australia Pty Ltd, Caringbah, NSW, Australia
| | - Tamar Jamieson
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia; Institute for Nanoscience and Technology, Flinders University, Bedford Park, SA, Australia
| | - Sophie C Leterme
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia; ARC Training Centre for Biofilm Research and Innovation, Flinders University, Bedford Park, SA, Australia; Institute for Nanoscience and Technology, Flinders University, Bedford Park, SA, Australia
| | - Harriet Whiley
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia; ARC Training Centre for Biofilm Research and Innovation, Flinders University, Bedford Park, SA, Australia.
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Jeewon R, Aullybux AA, Puchooa D, Nazurally N, Alrefaei AF, Zhang Y. Marine Microbial Polysaccharides: An Untapped Resource for Biotechnological Applications. Mar Drugs 2023; 21:420. [PMID: 37504951 PMCID: PMC10381399 DOI: 10.3390/md21070420] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/29/2023] Open
Abstract
As the largest habitat on Earth, the marine environment harbors various microorganisms of biotechnological potential. Indeed, microbial compounds, especially polysaccharides from marine species, have been attracting much attention for their applications within the medical, pharmaceutical, food, and other industries, with such interest largely stemming from the extensive structural and functional diversity displayed by these natural polymers. At the same time, the extreme conditions within the aquatic ecosystem (e.g., temperature, pH, salinity) may not only induce microorganisms to develop a unique metabolism but may also increase the likelihood of isolating novel polysaccharides with previously unreported characteristics. However, despite their potential, only a few microbial polysaccharides have actually reached the market, with even fewer being of marine origin. Through a synthesis of relevant literature, this review seeks to provide an overview of marine microbial polysaccharides, including their unique characteristics. In particular, their suitability for specific biotechnological applications and recent progress made will be highlighted before discussing the challenges that currently limit their study as well as their potential for wider applications. It is expected that this review will help to guide future research in the field of microbial polysaccharides, especially those of marine origin.
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Affiliation(s)
- Rajesh Jeewon
- Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, Réduit 80837, Mauritius
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Aadil Ahmad Aullybux
- Department of Agricultural and Food Science, Faculty of Agriculture, University of Mauritius, Réduit 80837, Mauritius
| | - Daneshwar Puchooa
- Department of Agricultural and Food Science, Faculty of Agriculture, University of Mauritius, Réduit 80837, Mauritius
| | - Nadeem Nazurally
- Department of Agricultural and Food Science, Faculty of Agriculture, University of Mauritius, Réduit 80837, Mauritius
| | - Abdulwahed Fahad Alrefaei
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ying Zhang
- School of Ecology and Natural Conservation, Beijing Forestry University, 35 East Qinghua Road, Haidian District, Beijing 100083, China
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Microbial Communities of Peaty Permafrost Tundra Soils along the Gradient of Environmental Conditions and Anthropogenic Disturbance in Pechora River Delta in the Eastern European Arctic. DIVERSITY 2023. [DOI: 10.3390/d15020251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Microbial communities play crucial roles in the global carbon cycle, particularly in peatland and tundra ecosystems experiencing climate change. The latest IPCC assessments highlight the anthropogenic changes in the Arctic peatlands and their consequences due to global climate change. These disturbances could trigger permafrost degradation and intensification of the biogeochemical processes resulting in greenhouse gas formation. In this study, we describe the variation in diversity and composition of soil microbial communities from shallow peat tundra sites with different anthropogenic loads and applied restoration interventions in the landscape of remnant fragments of terraces in the Pechora River delta, the Russian Arctic, Nenets Autonomous Okrug. The molecular approaches, including quantitative real-time PCR and high-throughput Illumina sequencing of 16S RNA and ITS, were applied to examine the bacterial and fungal communities in the soil samples. Anthropogenic disturbance leads to a significant decrease in the representation of Acidobacteria and Verrucomicrobia, while the proportion and diversity of Proteobacteria increase. Fungal communities in undisturbed sites may be characterized as monodominant, and anthropogenic impact increases the fungal diversity. Only the verrucomicrobial methanotrophs Methyloacifiphilaceae were found in the undisturbed sites, but proteobacterial methanotrophs Methylobacterium-Methylorubrum, as well as different methylotrophs affiliated with Methylophilaceae, and Beijerinckiaceae (Methylorosula), were detected in disturbed sites.
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Ngugi DK, Salcher MM, Andrei AS, Ghai R, Klotz F, Chiriac MC, Ionescu D, Büsing P, Grossart HP, Xing P, Priscu JC, Alymkulov S, Pester M. Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes. SCIENCE ADVANCES 2023; 9:eadc9392. [PMID: 36724220 PMCID: PMC9891703 DOI: 10.1126/sciadv.adc9392] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Ammonia-oxidizing archaea (AOA) play a key role in the aquatic nitrogen cycle. Their genetic diversity is viewed as the outcome of evolutionary processes that shaped ancestral transition from terrestrial to marine habitats. However, current genome-wide insights into AOA evolution rarely consider brackish and freshwater representatives or provide their divergence timeline in lacustrine systems. An unbiased global assessment of lacustrine AOA diversity is critical for understanding their origins, dispersal mechanisms, and ecosystem roles. Here, we leveraged continental-scale metagenomics to document that AOA species diversity in freshwater systems is remarkably low compared to marine environments. We show that the uncultured freshwater AOA, "Candidatus Nitrosopumilus limneticus," is ubiquitous and genotypically static in various large European lakes where it evolved 13 million years ago. We find that extensive proteome remodeling was a key innovation for freshwater colonization of AOA. These findings reveal the genetic diversity and adaptive mechanisms of a keystone species that has survived clonally in lakes for millennia.
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Affiliation(s)
- David Kamanda Ngugi
- Leibniz Institute DSMZ–German Collection of Cell Microorganisms and Cell Cultures GmbH, D-38124 Braunschweig, Germany
- Corresponding author.
| | - Michaela M. Salcher
- Institute of Hydrobiology, Biology Center CAS, Na Sádkách 7, 37005 České Budejovice, Czech Republic
| | - Adrian-Stefan Andrei
- Microbial Evogenomics Lab, Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Rohit Ghai
- Institute of Hydrobiology, Biology Center CAS, Na Sádkách 7, 37005 České Budejovice, Czech Republic
| | - Franziska Klotz
- Department of Biology, University of Konstanz, D-78457 Constance, Germany
| | - Maria-Cecilia Chiriac
- Institute of Hydrobiology, Biology Center CAS, Na Sádkách 7, 37005 České Budejovice, Czech Republic
| | - Danny Ionescu
- Department of Experimental Limnology, Leibniz Institute for Freshwater Ecology and Inland Fisheries, D-12587 Stechlin, Germany
| | - Petra Büsing
- Leibniz Institute DSMZ–German Collection of Cell Microorganisms and Cell Cultures GmbH, D-38124 Braunschweig, Germany
| | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz Institute for Freshwater Ecology and Inland Fisheries, D-12587 Stechlin, Germany
- Institute of Biochemistry and Biology, Potsdam University, D-14469 Potsdam, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Free University, D-14195 Berlin, Germany
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - John C. Priscu
- Department of Land Resources and Environmental Sciences, Montana State University, 334 Leon Johnson Hall, Bozeman, MT 59717, USA
| | - Salmor Alymkulov
- Institute of Physics, National Academy of Sciences of Kyrgyz Republic, Chui Avenue, 265-a, Bishkek 720071, Kyrgyzstan
| | - Michael Pester
- Leibniz Institute DSMZ–German Collection of Cell Microorganisms and Cell Cultures GmbH, D-38124 Braunschweig, Germany
- Institute of Microbiology, Technical University of Braunschweig, D-38108 Braunschweig, Germany
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10
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Aldholmi M, Ahmad R, Carretero‐Molina D, Pérez‐Victoria I, Martín J, Reyes F, Genilloud O, Gourbeyre L, Gefflaut T, Carlsson H, Maklakov A, O'Neill E, Field RA, Wilkinson B, O'Connell M, Ganesan A. Euglenatides, Potent Antiproliferative Cyclic Peptides Isolated from the Freshwater Photosynthetic Microalga Euglena gracilis. Angew Chem Int Ed Engl 2022; 61:e202203175. [PMID: 35325497 PMCID: PMC9321709 DOI: 10.1002/anie.202203175] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Indexed: 11/27/2022]
Abstract
By limiting the nitrogen source to glutamic acid, we isolated cyclic peptides from Euglena gracilis containing asparagine and non-proteinogenic amino acids. Structure elucidation was accomplished through spectroscopic methods, mass spectrometry and chemical degradation. The euglenatides potently inhibit pathogenic fungi and cancer cell lines e.g., euglenatide B exhibiting IC50 values of 4.3 μM in Aspergillus fumigatus and 0.29 μM in MCF-7 breast cancer cells. In an unprecedented convergence of non-ribosomal peptide synthetase and polyketide synthase assembly-line biosynthesis between unicellular species and the metazoan kingdom, euglenatides bear resemblance to nemamides from Caenorhabditis elegans and inhibited both producing organisms E. gracilis and C. elegans. By molecular network analysis, we detected over forty euglenatide-like metabolites in E. gracilis, E. sanguinea and E. mutabilis, suggesting an important biological role for these natural products.
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Affiliation(s)
- Mohammed Aldholmi
- Natural Products and Alternative MedicineCollege of Clinical PharmacyImam Abdulrahman Bin Faisal UniversityDammam31441Saudi Arabia
| | - Rizwan Ahmad
- Natural Products and Alternative MedicineCollege of Clinical PharmacyImam Abdulrahman Bin Faisal UniversityDammam31441Saudi Arabia
| | - Daniel Carretero‐Molina
- Fundación MEDINACentro de Excelencia en Investigación de Medicamentos Innovadores en AndalucíaAvenida del Conocimiento 3418016ArmillaGranadaSpain
| | - Ignacio Pérez‐Victoria
- Fundación MEDINACentro de Excelencia en Investigación de Medicamentos Innovadores en AndalucíaAvenida del Conocimiento 3418016ArmillaGranadaSpain
| | - Jesús Martín
- Fundación MEDINACentro de Excelencia en Investigación de Medicamentos Innovadores en AndalucíaAvenida del Conocimiento 3418016ArmillaGranadaSpain
| | - Fernando Reyes
- Fundación MEDINACentro de Excelencia en Investigación de Medicamentos Innovadores en AndalucíaAvenida del Conocimiento 3418016ArmillaGranadaSpain
| | - Olga Genilloud
- Fundación MEDINACentro de Excelencia en Investigación de Medicamentos Innovadores en AndalucíaAvenida del Conocimiento 3418016ArmillaGranadaSpain
| | - Léa Gourbeyre
- Université Clermont AuvergneClermont Auvergne INP, CNRS, Institut Pascal63000Clermont-FerrandFrance
| | - Thierry Gefflaut
- Université Clermont AuvergneClermont Auvergne INP, CNRS, Institut Pascal63000Clermont-FerrandFrance
| | - Hanne Carlsson
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Alexei Maklakov
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Ellis O'Neill
- School of ChemistryUniversity of NottinghamNottinghamNG7 2RDUK
| | - Robert A. Field
- Manchester Institute of BiotechnologyUniversity of ManchesterManchesterM1 7DNUK
| | | | - Maria O'Connell
- School of PharmacyUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - A. Ganesan
- School of PharmacyUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
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11
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Aldholmi M, Ahmad R, Carretero‐Molina D, Pérez‐Victoria I, Martín J, Reyes F, Genilloud O, Gourbeyre L, Gefflaut T, Carlsson H, Maklakov A, O'Neill E, Field RA, Wilkinson B, O'Connell M, Ganesan A. Euglenatides, Potent Antiproliferative Cyclic Peptides Isolated from the Freshwater Photosynthetic Microalga
Euglena gracilis. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mohammed Aldholmi
- Natural Products and Alternative Medicine College of Clinical Pharmacy Imam Abdulrahman Bin Faisal University Dammam 31441 Saudi Arabia
| | - Rizwan Ahmad
- Natural Products and Alternative Medicine College of Clinical Pharmacy Imam Abdulrahman Bin Faisal University Dammam 31441 Saudi Arabia
| | - Daniel Carretero‐Molina
- Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Avenida del Conocimiento 34 18016 Armilla Granada Spain
| | - Ignacio Pérez‐Victoria
- Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Avenida del Conocimiento 34 18016 Armilla Granada Spain
| | - Jesús Martín
- Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Avenida del Conocimiento 34 18016 Armilla Granada Spain
| | - Fernando Reyes
- Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Avenida del Conocimiento 34 18016 Armilla Granada Spain
| | - Olga Genilloud
- Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía Avenida del Conocimiento 34 18016 Armilla Granada Spain
| | - Léa Gourbeyre
- Université Clermont Auvergne Clermont Auvergne INP, CNRS, Institut Pascal 63000 Clermont-Ferrand France
| | - Thierry Gefflaut
- Université Clermont Auvergne Clermont Auvergne INP, CNRS, Institut Pascal 63000 Clermont-Ferrand France
| | - Hanne Carlsson
- School of Biological Sciences University of East Anglia Norwich Research Park Norwich NR4 7TJ UK
| | - Alexei Maklakov
- School of Biological Sciences University of East Anglia Norwich Research Park Norwich NR4 7TJ UK
| | - Ellis O'Neill
- School of Chemistry University of Nottingham Nottingham NG7 2RD UK
| | - Robert A. Field
- Manchester Institute of Biotechnology University of Manchester Manchester M1 7DN UK
| | | | - Maria O'Connell
- School of Pharmacy University of East Anglia Norwich Research Park Norwich NR4 7TJ UK
| | - A. Ganesan
- School of Pharmacy University of East Anglia Norwich Research Park Norwich NR4 7TJ UK
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12
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Moura JB, Delforno TP, do Prado PF, Duarte IC. Extremophilic taxa predominate in a microbial community of photovoltaic panels in a tropical region. FEMS Microbiol Lett 2021; 368:6350555. [PMID: 34387344 DOI: 10.1093/femsle/fnab105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/10/2021] [Indexed: 12/25/2022] Open
Abstract
Photovoltaic panels can be colonized by a highly diverse microbial diversity, despite life-threatening conditions. Although they are distributed worldwide, the microorganisms living on their surfaces have never been profiled in tropical regions using 16S rRNA high-throughput sequencing and PICRUst metagenome prediction of functional content. In this work, we investigated photovoltaic panels from two cities in southeast Brazil, Sorocaba and Itatiba, using these bioinformatics approach. Results showed that, despite significant differences in microbial diversity (p < 0.001), the taxonomic profile was very similar for both photovoltaic panels, dominated mainly by Proteobacteria, Bacteroidota and lower amounts of Cyanobacteria phyla. A predominance of Hymenobacter and Methylobacterium-Methylorubrum was observed at the genus level. We identified a microbial common core composed of Hymenobacter, Deinococcus, Sphingomonas, Methylobacterium-Methylorubrum, Craurococcus-Caldovatus, Massilia, Noviherbaspirillum and 1174-901-12 sharing genera. Predicted metabolisms focused on specific genes associated to radiation and desiccation resistance and pigments, were detected in members of the common core and among the most abundant genera. Our results suggested that taxonomic and functional profiles investigated were consistent with the harsh environment that photovoltaic panels represent. Moreover, the presence of stress genes in the predicted functional content was a preliminary evidence that microbes living there are a possibly source of metabolites with biotechnological interest.
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Affiliation(s)
- Juliane B Moura
- Department of Biology, Laboratory of Applied Microbiology, Federal University of São Carlos, Rodovia João Leme dos Santos km 110, Itinga 18052-780, Sorocaba-SP, Brazil
| | - Tiago P Delforno
- SENAI Innovation Institute for Biotechnology, Rua Anhaia, 1321, Bom Retiro, São Paulo 01130-000, São Paulo-SP, Brazil
| | - Pierre F do Prado
- Earth Physics and Thermodynamics Department, University of Valencia, C/Dr Moliner n 50, 46010 Burjassot, Valencia, Spain
| | - Iolanda C Duarte
- Department of Biology, Laboratory of Applied Microbiology, Federal University of São Carlos, Rodovia João Leme dos Santos km 110, Itinga 18052-780, Sorocaba-SP, Brazil
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13
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Metagenome-Assembled Genomes Contribute to Unraveling of the Microbiome of Cocoa Fermentation. Appl Environ Microbiol 2021; 87:e0058421. [PMID: 34105982 DOI: 10.1128/aem.00584-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Metagenomic studies about cocoa fermentation have mainly reported on the analysis of short reads for determination of operational taxonomic units. However, it is also important to determine metagenome-assembled genomes (MAGs), which are genomes deriving from the assembly of metagenomics. For this research, all the cocoa metagenomes from public databases were downloaded, resulting in five data sets: one from Ghana and four from Brazil. In addition, in silico approaches were used to describe putative phenotypes and the metabolic potential of MAGs. A total of 17 high-quality MAGs were recovered from these microbiomes, as follows: (i) for fungi, Yamadazyma tenuis (n = 1); (ii) lactic acid bacteria, Limosilactobacillus fermentum (n = 5), Liquorilactobacillus cacaonum (n = 1), Liquorilactobacillus nagelli (n = 1), Leuconostoc pseudomesenteroides (n = 1), and Lactiplantibacillus plantarum subsp. plantarum (n = 1); (iii) acetic acid bacteria, Acetobacter senegalensis (n = 2) and Kozakia baliensis (n = 1); and (iv) Bacillus subtilis (n = 1), Brevundimonas sp. (n = 2), and Pseudomonas sp. (n = 1). Medium-quality MAGs were also recovered from cocoa microbiomes, including some that, to our knowledge, were not previously detected in this environment (Liquorilactobacillus vini, Komagataeibacter saccharivorans, and Komagataeibacter maltaceti) and others previously described (Fructobacillus pseudoficulneus and Acetobacter pasteurianus). Taken together, the MAGs were useful for providing an additional description of the microbiome of cocoa fermentation, revealing previously overlooked microorganisms, with prediction of key phenotypes and biochemical pathways. IMPORTANCE The production of chocolate starts with the harvesting of cocoa fruits and the spontaneous fermentation of the seeds in a microbial succession that depends on yeasts, lactic acid bacteria, and acetic acid bacteria in order to eliminate bitter and astringent compounds present in the raw material, which will be further roasted and grinded to originate the cocoa powder that will enter the food processing industry. The microbiota of cocoa fermentation is not completely known, and yet it advanced from culture-based studies to the advent of next-generation DNA sequencing, with the generation of a myriad of data that need bioinformatic approaches to be properly analyzed. Although the majority of metagenomic studies have been based on short reads (operational taxonomic units), it is also important to analyze entire genomes to determine more precisely possible ecological roles of different species. Metagenome-assembled genomes (MAGs) are very useful for this purpose; here, MAGs from cocoa fermentation microbiomes are described, and the possible implications of their phenotypic and metabolic potentials are discussed.
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14
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Schiaffino MR, Huber P, Sagua M, Sabio Y García CA, Reissig M. Covariation patterns of phytoplankton and bacterioplankton in hypertrophic shallow lakes. FEMS Microbiol Ecol 2020; 96:5894912. [PMID: 32816009 DOI: 10.1093/femsec/fiaa161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 08/12/2020] [Indexed: 11/14/2022] Open
Abstract
The aim of this work was to assess the temporal patterns in the community composition of phytoplankton (PCC) and bacterioplankton (BCC) in two interconnected and hypertrophic Pampean shallow lakes in Argentina. Factors shaping their community dynamics and community temporal covariations were also analysed. We performed 4 years of seasonal samplings (2012-2016) and communities were studied by the Utermöhl approach (PCC) and Illumina MiSeq sequencing (BCC). We found marked seasonal variations in both communities and inter-annual variations with decreasing microbial community similarities during the study. We also observed covariation in community-level dynamics among PCC and BCC within and between shallow lakes. The within-lake covariations remained positive and significant, while controlling for the effects of intrinsic (environmental) and extrinsic (temporal and meteorological) factors, suggesting a community coupling mediated by intrinsic biotic interactions. Algal-bacterial associations between different taxa of phytoplankton and bacterioplankton within each lake were also found. PCC was mainly explained by pure regional extrinsic (17-21%) and intrinsic environmental (8-9%) factors, while BCC was explained by environmental (8-10%) and biotic interactions with phytoplankton (7-8%). Our results reveal that the influence of extrinsic regional factors can be channeled to bacterioplankton through both environmental (i.e. water temperature) and phytoplankton effects.
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Affiliation(s)
- M R Schiaffino
- Departamento de Ciencias Básicas y Experimentales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Roque Sáenz Peña 456, 6000, Junín, Argentina.,Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CITNOBA) - UNNOBA-UNSAdA-CONICET, Jorge Newbery 355, 6000, Junín, Argentina
| | - P Huber
- Instituto Nacional de Limnología (INALI, CONICET-UNL), Colectora Ruta Nac. 168, Paraje El Pozo, 3000, Santa Fe, Argentina
| | - M Sagua
- Departamento de Ciencias Básicas y Experimentales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Roque Sáenz Peña 456, 6000, Junín, Argentina.,Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CITNOBA) - UNNOBA-UNSAdA-CONICET, Jorge Newbery 355, 6000, Junín, Argentina
| | - C A Sabio Y García
- CONICET - Universidad de Buenos Aires, Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Intendente Güiraldes 2160, Ciudad Universitaria - C1428EGA, Buenos Aires, Argentina.,Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Depto. Ecología, Genética y Evolución, Intendente Güiraldes 2160, Ciudad Universitaria - C1428EGA, Buenos Aires, Argentina
| | - M Reissig
- Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA), Universidad Nacional del Comahue - CONICET, Quintral 1250, 8400, San Carlos de Bariloche, Argentina
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15
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Wang C, Masoudi A, Wang M, Yang J, Shen R, Man M, Yu Z, Liu J. Community structure and diversity of the microbiomes of two microhabitats at the root-soil interface: implications of meta-analysis of the root-zone soil and root endosphere microbial communities in Xiong'an New Area. Can J Microbiol 2020; 66:605-622. [PMID: 32526152 DOI: 10.1139/cjm-2020-0061] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The diversity of the microbial compositions of the root-zone soil (the rhizosphere-surrounding soil) and root endosphere (all inner root tissues) of Pinus tabulaeformis Carr. and Ginkgo biloba L. were evaluated in Xiong'an New Area using high-throughput sequencing; the influence of the soil edaphic parameters on microbial community compositions was also evaluated. Our results showed that both the taxonomic and phylogenetic diversities of the root endosphere were lower than those of the root-zone soil, but the variation in the endosphere microbial community structure was remarkably higher than that of the root-zone soil. Spearman correlation analysis showed that the soil organic matter, total nitrogen, total phosphate, total potassium, ratio of carbon to nitrogen, and pH significantly explained the α-diversity of the bacterial community and that total nitrogen differentially contributed to the α-diversity of the fungal community. Variation partitioning analysis showed that plant species had a greater influence on microbial composition variations than did any other soil property, although soil chemical parameters explained more variation when integrated. Together, our results suggest that both plant species and soil chemical parameters played a critical role in shaping the microbial community composition.
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Affiliation(s)
- Can Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P.R. China
| | - Abolfazl Masoudi
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P.R. China
| | - Min Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P.R. China
| | - Jia Yang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P.R. China
| | - Ruowen Shen
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P.R. China
| | - Meng Man
- Library of Hebei Normal University, Hebei Normal University, Shijiazhuang 050024, P.R. China
| | - Zhijun Yu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P.R. China
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P.R. China
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16
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Gonçalves CC, Bruce T, Silva CDOG, Fillho EXF, Noronha EF, Carlquist M, Parachin NS. Bioprospecting Microbial Diversity for Lignin Valorization: Dry and Wet Screening Methods. Front Microbiol 2020; 11:1081. [PMID: 32582068 PMCID: PMC7295907 DOI: 10.3389/fmicb.2020.01081] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/30/2020] [Indexed: 01/02/2023] Open
Abstract
Lignin is an abundant cell wall component, and it has been used mainly for generating steam and electricity. Nevertheless, lignin valorization, i.e. the conversion of lignin into high value-added fuels, chemicals, or materials, is crucial for the full implementation of cost-effective lignocellulosic biorefineries. From this perspective, rapid screening methods are crucial for time- and resource-efficient development of novel microbial strains and enzymes with applications in the lignin biorefinery. The present review gives an overview of recent developments and applications of a vast arsenal of activity and sequence-based methodologies for uncovering novel microbial strains with ligninolytic potential, novel enzymes for lignin depolymerization and for unraveling the main metabolic routes during growth on lignin. Finally, perspectives on the use of each of the presented methods and their respective advantages and disadvantages are discussed.
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Affiliation(s)
- Carolyne Caetano Gonçalves
- Department of Genomic Science and Biotechnology, Universidade Católica de Brasília - UCB, Brasília, Brazil
| | - Thiago Bruce
- Department of Genomic Science and Biotechnology, Universidade Católica de Brasília - UCB, Brasília, Brazil
| | | | | | - Eliane Ferreira Noronha
- Laboratory of Enzymology, Department of Cellular Biology, University of Brasília, Brasília, Brazil
| | - Magnus Carlquist
- Division of Applied Microbiology, Department of Chemistry, Faculty of Engineering, Lund University, Lund, Sweden
| | - Nádia Skorupa Parachin
- Department of Genomic Science and Biotechnology, Universidade Católica de Brasília - UCB, Brasília, Brazil
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17
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Rosa, Luiz Henrique Rosa (ed): Fungi of Antarctica: diversity, ecology and biotechnological applications. Polar Biol 2020. [DOI: 10.1007/s00300-019-02619-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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18
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Accessing the Life in Smoke: A New Application of Unmanned Aircraft Systems (UAS) to Sample Wildland Fire Bioaerosol Emissions and Their Environment. FIRE-SWITZERLAND 2019. [DOI: 10.3390/fire2040056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Wildland fire is a major producer of aerosols from combustion of vegetation and soils, but little is known about the abundance and composition of smoke’s biological content. Bioaerosols, or aerosols derived from biological sources, may be a significant component of the aerosol load vectored in wildland fire smoke. If bioaerosols are injected into the upper troposphere via high-intensity wildland fires and transported across continents, there may be consequences for the ecosystems they reach. Such transport would also alter the concept of a wildfire’s perimeter and the disturbance domain of its impact. Recent research has revealed that viable microorganisms are directly aerosolized during biomass combustion, but sampling systems and methodology for quantifying this phenomenon are poorly developed. Using a series of prescribed fires in frequently burned forest ecosystems, we report the results of employing a small rotary-wing unmanned aircraft system (UAS) to concurrently sample aerosolized bacteria and fungi, particulate matter, and micrometeorology in smoke plumes versus background conditions. Airborne impaction-based bioaerosol sampling indicated that microbial composition differed between background air and smoke, with seven unique organisms in smoke vs. three in background air. The air temperature was negatively correlated with the number of fungal colony-forming units detected. Our results demonstrate the utility of a UAS-based sampling platform for active sampling of viable aerosolized microbes in smoke arising from wildland fires. This methodology can be extended to sample viable microbes in a wide variety of emissions sampling pursuits, especially those in hazardous and inaccessible environments.
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19
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Purohit HJ. Aligning Microbial Biodiversity for Valorization of Biowastes: Conception to Perception. Indian J Microbiol 2019; 59:391-400. [PMID: 31762500 DOI: 10.1007/s12088-019-00826-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/12/2019] [Indexed: 12/16/2022] Open
Abstract
Generation of biowastes is increasing rapidly and its uncontrolled, slow and persistent fermentation leads to the release of Green-house gases (GHGs) into the environment. Exploration and exploitation of microbial diversity for degrading biowastes can result in producing diverse range of bioactive molecules, which can act as a source of bioenergy, biopolymers, nutraceuticals and antimicrobials. The whole process is envisaged to manage biowastes, and reduce their pollution causing capacity, and lead to a sustainable society. A strategy has been proposed for: (1) producing bioactive molecules, and (2) achieving a zero-pollution emission by recycling of the GHGs through biological routes.
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Affiliation(s)
- Hemant J Purohit
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental and Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, Maharashtra 440020 India
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20
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Rapacciuolo G, Beman JM, Schiebelhut LM, Dawson MN. Microbes and macro-invertebrates show parallel β-diversity but contrasting α-diversity patterns in a marine natural experiment. Proc Biol Sci 2019; 286:20190999. [PMID: 31594510 DOI: 10.1098/rspb.2019.0999] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Documenting ecological patterns across spatially, temporally and taxonomically diverse ecological communities is necessary for a general understanding of the processes shaping biodiversity. A major gap in our understanding remains the comparison of diversity patterns across a broad spectrum of evolutionarily and functionally diverse organisms, particularly in the marine realm. Here, we aim to narrow this gap by comparing the diversity patterns of free-living microbes and macro-invertebrates across a natural experiment provided by the marine lakes of Palau: geographically discrete and environmentally heterogeneous bodies of seawater with comparable geological and climatic history, and a similar regional species pool. We find contrasting patterns of α-diversity but remarkably similar patterns of β-diversity between microbial and macro-invertebrate communities among lakes. Pairwise dissimilarities in community composition among lakes are positively correlated between microbes and macro-invertebrates, and influenced to a similar degree by marked gradients in oxygen concentration and salinity. Our findings indicate that a shared spatio-temporal and environmental context may result in parallel patterns of β-diversity in microbes and macro-invertebrates, in spite of key trait differences between these organisms. This raises the possibility that parallel processes also influence transitions among regional biota across the tree of life, at least in the marine realm.
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Affiliation(s)
- Giovanni Rapacciuolo
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, CA, USA.,Life and Environmental Sciences, University of California Merced, Merced, CA, USA
| | - J Michael Beman
- Life and Environmental Sciences, University of California Merced, Merced, CA, USA
| | - Lauren M Schiebelhut
- Life and Environmental Sciences, University of California Merced, Merced, CA, USA
| | - Michael N Dawson
- Life and Environmental Sciences, University of California Merced, Merced, CA, USA
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