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Jurburg SD, Blowes SA, Shade A, Eisenhauer N, Chase JM. Synthesis of recovery patterns in microbial communities across environments. MICROBIOME 2024; 12:79. [PMID: 38711157 DOI: 10.1186/s40168-024-01802-3] [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: 12/08/2023] [Accepted: 03/25/2024] [Indexed: 05/08/2024]
Abstract
BACKGROUND Disturbances alter the diversity and composition of microbial communities. Yet a generalized empirical assessment of microbiome responses to disturbance across different environments is needed to understand the factors driving microbiome recovery, and the role of the environment in driving these patterns. RESULTS To this end, we combined null models with Bayesian generalized linear models to examine 86 time series of disturbed mammalian, aquatic, and soil microbiomes up to 50 days following disturbance. Overall, disturbances had the strongest effect on mammalian microbiomes, which lost taxa and later recovered their richness, but not their composition. In contrast, following disturbance, aquatic microbiomes tended away from their pre-disturbance composition over time. Surprisingly, across all environments, we found no evidence of increased compositional dispersion (i.e., variance) following disturbance, in contrast to the expectations of the Anna Karenina Principle. CONCLUSIONS This is the first study to systematically compare secondary successional dynamics across disturbed microbiomes, using a consistent temporal scale and modeling approach. Our findings show that the recovery of microbiomes is environment-specific, and helps to reconcile existing, environment-specific research into a unified perspective. Video Abstract.
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Affiliation(s)
- Stephanie D Jurburg
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany.
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany.
- Institute of Biology, Leipzig University, 04103, Leipzig, Germany.
| | - Shane A Blowes
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
- Institute of Computer Science, Martin-Luther University Halle-Wittenberg, 06108, Halle (Saale), Halle, Germany
| | - Ashley Shade
- Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Universite Claude Bernard Lyon 1, 69622, Villeurbanne, France
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, 04103, Leipzig, Germany
| | - Jonathan M Chase
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
- Institute of Computer Science, Martin-Luther University Halle-Wittenberg, 06108, Halle (Saale), Halle, Germany
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Romantschuk M, Lahti-Leikas K, Kontro M, Galitskaya P, Talvenmäki H, Simpanen S, Allen JA, Sinkkonen A. Bioremediation of contaminated soil and groundwater by in situ biostimulation. Front Microbiol 2023; 14:1258148. [PMID: 38029190 PMCID: PMC10658714 DOI: 10.3389/fmicb.2023.1258148] [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: 07/13/2023] [Accepted: 09/22/2023] [Indexed: 12/01/2023] Open
Abstract
Bioremediation by in situ biostimulation is an attractive alternative to excavation of contaminated soil. Many in situ remediation methods have been tested with some success; however, due to highly variable results in realistic field conditions, they have not been implemented as widely as they might deserve. To ensure success, methods should be validated under site-analogous conditions before full scale use, which requires expertise and local knowledge by the implementers. The focus here is on indigenous microbial degraders and evaluation of their performance. Identifying and removing biodegradation bottlenecks for degradation of organic pollutants is essential. Limiting factors commonly include: lack of oxygen or alternative electron acceptors, low temperature, and lack of essential nutrients. Additional factors: the bioavailability of the contaminating compound, pH, distribution of the contaminant, and soil structure and moisture, and in some cases, lack of degradation potential which may be amended with bioaugmentation. Methods to remove these bottlenecks are discussed. Implementers should also be prepared to combine methods or use them in sequence. Chemical/physical means may be used to enhance biostimulation. The review also suggests tools for assessing sustainability, life cycle assessment, and risk assessment. To help entrepreneurs, decision makers, and methods developers in the future, we suggest founding a database for otherwise seldom reported unsuccessful interventions, as well as the potential for artificial intelligence (AI) to assist in site evaluation and decision-making.
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Affiliation(s)
- Martin Romantschuk
- Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Katariina Lahti-Leikas
- Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Merja Kontro
- Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | | | - Harri Talvenmäki
- Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Suvi Simpanen
- Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - John A. Allen
- Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Aki Sinkkonen
- Natural Resources Institute Finland (Luke), Horticulture Technologies, Turku, Finland
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Sulbaran-Bracho Y, Orellana-Saez M, Castro-Severyn J, Galbán-Malagón C, Castro-Nallar E, Poblete-Castro I. Continuous bioreactors enable high-level bioremediation of diesel-contaminated seawater at low and mesophilic temperatures using Antarctic bacterial consortia: Pollutant analysis and microbial community composition. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 321:121139. [PMID: 36702434 DOI: 10.1016/j.envpol.2023.121139] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 01/15/2023] [Accepted: 01/21/2023] [Indexed: 06/18/2023]
Abstract
In 2020, more than 21,000 tons of diesel oil were released accidently into the environment with most of it contaminating water bodies. There is an urgent need for sustainable technologies to clean up rivers and oceans to protect wildlife and human health. One solution is harnessing the power of bacterial consortia; however isolated microbes from different environments have shown low diesel bioremediation rates in seawater thus far. An outstanding question is whether Antarctic microorganisms that thrive in environments polluted with hydrocarbons exhibit better diesel degrading activities when propagated at higher temperatures than those encountered in their natural ecosystems. Here, we isolated bacterial consortia, LR-30 (30 °C) and LR-10 (10 °C), from the Antarctic rhizosphere soil of Deschampsia antarctica (Livingston Island), that used diesel oil as the only carbon substrate. We found that LR-30 and LR-10 batch bioreactors metabolized nearly the entire diesel content when the initial concentration was 10 (g/L) in seawater. Increasing the initial diesel concentration to 50 gDiesel/L, LR-30 and LR-10 bioconverted 33.4 and 31.2 gDiesel/L in 7 days, respectively. The 16S rRNA gene sequencing profiles revealed that the dominant bacterial genera of the inoculated LR-30 community were Achromobacter (50.6%), Pseudomonas (25%) and Rhodanobacter (14.9%), whereas for LR-10 were Pseudomonas (58%), Candidimonas (10.3%) and Renibacterium (7.8%). We also established continuous bioreactors for diesel biodegradation where LR-30 bioremediated diesel at an unprecedent rate of (34.4 g/L per day), while LR-10 achieved (24.5 g/L per day) at 10 °C for one month. The abundance of each bacterial genera present significantly fluctuated at some point during the diesel bioremediation process, yet Achromobacter and Pseudomonas were the most abundant member at the end of the batch and continuous bioreactors for LR-30 and LR-10, respectively.
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Affiliation(s)
- Yoelvis Sulbaran-Bracho
- Biosystems Engineering Laboratory, Department of Chemical and Bioprocess Engineering, Faculty of Engineering, Universidad de Santiago de Chile (USACH), 9170022, Santiago, Chile
| | - Matias Orellana-Saez
- Biosystems Engineering Laboratory, Department of Chemical and Bioprocess Engineering, Faculty of Engineering, Universidad de Santiago de Chile (USACH), 9170022, Santiago, Chile
| | - Juan Castro-Severyn
- Laboratorio de Microbiología Aplicada Y Extremófilos, Facultad de Ingeniería Y Ciencias Geológicas, Universidad Católica Del Norte, Antofagasta, Chile
| | - Cristóbal Galbán-Malagón
- GEMA, Center for Genomics, Ecology & Environment, Universidad Mayor, Camino La Pirámide, 5750, Huechuraba, Santiago, Chile
| | - Eduardo Castro-Nallar
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Campus Talca, Avda. Lircay s/n, Talca, Chile; Centro de Ecología Integrativa, Universidad de Talca, Campus Talca, Avda. Lircay s/n, Talca, Chile
| | - Ignacio Poblete-Castro
- Biosystems Engineering Laboratory, Department of Chemical and Bioprocess Engineering, Faculty of Engineering, Universidad de Santiago de Chile (USACH), 9170022, Santiago, Chile.
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Liu X, Li X, Hua Y, Sinkkonen A, Romantschuk M, Lv Y, Wu Q, Hui N. Meat and bone meal stimulates microbial diversity and suppresses plant pathogens in asparagus straw composting. Front Microbiol 2022; 13:953783. [PMID: 36204619 PMCID: PMC9530395 DOI: 10.3389/fmicb.2022.953783] [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: 05/26/2022] [Accepted: 08/15/2022] [Indexed: 11/20/2022] Open
Abstract
Meat and bone meal (MBM), as slaughterhouse waste, is a potential biostimulating agent, but its efficiency and reliability in composting are largely unknown. To access the MBM application to the composting process of asparagus straw rice, we followed the composting process for 60 days in 220-L composters and another 180 days in 20-L buckets in treatments applied with MBM or urea. The microbial succession was investigated by high-throughput sequencing. Compared with urea treatments, MBM addition stabilized pH and extended the thermophilic phase for 7 days. The germination index of MBM treatments was 24.76% higher than that of urea treatments. MBM also promoted higher microbial diversity and shifted community compositions. Organic matter and pH were the most significant factors that influence the bacterial and fungal community structure. At the genus level, MBM enriched relative abundances of organic matter-degrading bacteria (Alterococcus) and lignocellulose-degrading fungi (Trichoderma), as well as lignocellulolytic enzyme activities. Notably, MBM addition decreased sum abundances of plant pathogenic fungi of Phaeoacremonium, Acremonium, and Geosmithia from 17.27 to 0.11%. This study demonstrated the potential of MBM as an effective additive in asparagus straw composting, thus providing insights into the development of new industrial aerobic fermentation.
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Affiliation(s)
- Xinxin Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, Shanghai, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, Shanghai, China
| | - Xiaoxiao Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yinfeng Hua
- Shanghai Pudong Development (Group) CO., Ltd., Shanghai, China
| | - Aki Sinkkonen
- Department of Garden Technologies, Horticulture Technologies, Natural Resources Institute Finland, Helsinki, Finland
| | - Martin Romantschuk
- Faculty of Biological and Environmental Science, University of Helsinki, Lahti, Finland
| | - Yanfang Lv
- Food Safety Key Lab of Liaoning Province, College of Food Science and Engineering, Bohai University, Jinzhou, China
| | - Qian Wu
- Boda Environmental Protection Co., Ltd., Yixing, China
| | - Nan Hui
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Faculty of Biological and Environmental Science, University of Helsinki, Lahti, Finland
- *Correspondence: Nan Hui
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Habitat Elevation Shapes Microbial Community Composition and Alter the Metabolic Functions in Wild Sable ( Martes zibellina) Guts. Animals (Basel) 2021; 11:ani11030865. [PMID: 33803658 PMCID: PMC8002971 DOI: 10.3390/ani11030865] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/10/2021] [Accepted: 03/14/2021] [Indexed: 12/11/2022] Open
Abstract
In recent decades, wild sable (Carnivora Mustelidae Martes zibellina) habitats, which are often natural forests, have been squeezed by anthropogenic disturbances such as clear-cutting, tilling and grazing. Sables tend to live in sloped areas with relatively harsh conditions. Here, we determine effects of environmental factors on wild sable gut microbial communities between high and low altitude habitats using Illumina Miseq sequencing of bacterial 16S rRNA genes. Our results showed that despite wild sable gut microbial community diversity being resilient to many environmental factors, community composition was sensitive to altitude. Wild sable gut microbial communities were dominated by Firmicutes (relative abundance 38.23%), followed by Actinobacteria (30.29%), and Proteobacteria (28.15%). Altitude was negatively correlated with the abundance of Firmicutes, suggesting sable likely consume more vegetarian food in lower habitats where plant diversity, temperature and vegetation coverage were greater. In addition, our functional genes prediction and qPCR results demonstrated that energy/fat processing microorganisms and functional genes are enriched with increasing altitude, which likely enhanced metabolic functions and supported wild sables to survive in elevated habitats. Overall, our results improve the knowledge of the ecological impact of habitat change, providing insights into wild animal protection at the mountain area with hash climate conditions.
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