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Arnolds KL, Higgins RC, Crandall J, Li G, Linger JG, Guarnieri MT. Risk Assessment of Industrial Microbes Using a Terrestrial Mesocosm Platform. MICROBIAL ECOLOGY 2023; 87:12. [PMID: 38072911 PMCID: PMC10710964 DOI: 10.1007/s00248-023-02321-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/24/2023] [Indexed: 12/18/2023]
Abstract
Industrial microbes and bio-derived products have emerged as an integral component of the bioeconomy, with an array of agricultural, bioenergy, and biomedical applications. However, the rapid development of microbial biotechnology raises concerns related to environmental escape of laboratory microbes, detection and tracking thereof, and resultant impact upon native ecosystems. Indeed, though wild-type and genetically modified microbes are actively deployed in industrial bioprocesses, an understanding of microbial interactivity and impact upon the environment is severely lacking. In particular, the persistence and sustained ecosystem impact of industrial microbes following laboratory release or unintentional laboratory escape remains largely unexplored. Herein, we investigate the applicability of soil-sorghum mesocosms for the ecological risk assessment of the industrial microbe, Saccharomyces cerevisiae. We developed and applied a suite of diagnostic and bioinformatic analyses, including digital droplet PCR, microscopy, and phylogenomic analyses to assess the impacts of a terrestrial ecosystem perturbation event over a 30-day time course. The platform enables reproducible, high-sensitivity tracking of S. cerevisiae in a complex soil microbiome and analysis of the impact upon abiotic soil characteristics and soil microbiome population dynamics and diversity. The resultant data indicate that even though S. cerevisiae is relatively short-lived in the soil, a single perturbation event can have sustained impact upon mesocosm soil composition and underlying microbial populations in our system, underscoring the necessity for more comprehensive risk assessment and development of mitigation and biocontainment strategies in industrial bioprocesses.
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Affiliation(s)
- Kathleen L Arnolds
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Pkwy, Golden, CO, 80401, USA
| | - Riley C Higgins
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Pkwy, Golden, CO, 80401, USA
| | - Jennifer Crandall
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Pkwy, Golden, CO, 80401, USA
| | - Gabriella Li
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Pkwy, Golden, CO, 80401, USA
| | - Jeffrey G Linger
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Pkwy, Golden, CO, 80401, USA
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Michael T Guarnieri
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Pkwy, Golden, CO, 80401, USA.
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO, 80401, USA.
- Renewable & Sustainable Energy Institute, University of Colorado, Boulder, CO, 80303, USA.
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Jech SD, Day N, Barger NN, Antoninka A, Bowker MA, Reed S, Tucker C. Cultivating Resilience in Dryland Soils: An Assisted Migration Approach to Biological Soil Crust Restoration. Microorganisms 2023; 11:2570. [PMID: 37894228 PMCID: PMC10608944 DOI: 10.3390/microorganisms11102570] [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: 07/31/2023] [Revised: 10/01/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023] Open
Abstract
Land use practices and climate change have driven substantial soil degradation across global drylands, impacting ecosystem functions and human livelihoods. Biological soil crusts, a common feature of dryland ecosystems, are under extensive exploration for their potential to restore the stability and fertility of degraded soils through the development of inoculants. However, stressful abiotic conditions often result in the failure of inoculation-based restoration in the field and may hinder the long-term success of biocrust restoration efforts. Taking an assisted migration approach, we cultivated biocrust inocula sourced from multiple hot-adapted sites (Mojave and Sonoran Deserts) in an outdoor facility at a cool desert site (Colorado Plateau). In addition to cultivating inoculum from each site, we created an inoculum mixture of biocrust from the Mojave Desert, Sonoran Desert, and Colorado Plateau. We then applied two habitat amelioration treatments to the cultivation site (growth substrate and shading) to enhance soil stability and water availability and reduce UV stress. Using marker gene sequencing, we found that the cultivated mixed inoculum comprised both local- and hot-adapted cyanobacteria at the end of cultivation but had similar cyanobacterial richness as each unmixed inoculum. All cultivated inocula had more cyanobacterial 16S rRNA gene copies and higher cyanobacterial richness when cultivated with a growth substrate and shade. Our work shows that it is possible to field cultivate biocrust inocula sourced from different deserts, but that community composition shifts toward that of the cultivation site unless habitat amelioration is employed. Future assessments of the function of a mixed inoculum in restoration and its resilience in the face of abiotic stressors are needed to determine the relative benefit of assisted migration compared to the challenges and risks of this approach.
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Affiliation(s)
- Sierra D Jech
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Natalie Day
- Colorado Water Science Center, U.S. Geological Survey, Grand Junction, CO 81506, USA
| | - Nichole N Barger
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Anita Antoninka
- School of Forestry, Northern Arizona University, Flagstaff, AZ 86001, USA
| | - Matthew A Bowker
- School of Forestry, Northern Arizona University, Flagstaff, AZ 86001, USA
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86001, USA
| | - Sasha Reed
- Southwest Biological Science Center, U.S. Geological Survey, Moab, UT 84532, USA
| | - Colin Tucker
- Manti-La Sal National Forest, U.S. Forest Service, Monticello, UT 84535, USA
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Palmer B, Lawson D, Lipson DA. Years After a Fire, Biocrust Microbial Communities are Similar to Unburned Communities in a Coastal Grassland. MICROBIAL ECOLOGY 2023; 85:1028-1044. [PMID: 36346444 PMCID: PMC10156770 DOI: 10.1007/s00248-022-02137-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 10/24/2022] [Indexed: 05/04/2023]
Abstract
Microbial communities are integral for ecosystem processes and their taxonomic composition and function may be altered by a disturbance such as fire. Biocrusts are composed of macroscopic and microscopic organisms and are important for a variety of ecosystem functions, such as nutrient cycling and erosion control. We sought to understand if biocrust community composition and function were altered 1 year after a prescribed fire and 6 years after a wildfire in a coastal California grassland on San Clemente Island. We used shotgun metagenomic sequencing and measurements of chlorophyll content, exopolysaccharide production related to soil stability, and nitrogen fixation. There were no differences in the community composition between unburned samples and the samples burned in the prescribed fire and wildfire. Chlorophyll content differed between the prescribed fire and the controls; however, there were no measured differences in exopolysaccharide production, and nitrogen fixation. However, the wildfire and their respective unburned samples had different functions based on the gene annotations. We compiled one Actinobacteria metagenome-assembled genome from the shotgun sequences which had genes for oxidative and heat stress tolerance. These results suggest that the biocrust community can reach a community composition and function similar to the unburned biocrusts within a year after a prescribed burn and 6 years after a wildfire. However, legacy effects of the wildfire may present themselves in the differences between functional gene sequences. Due to their ability to match the undisturbed community composition and function within years and without intervention, future restoration work should consider the biocrusts in their restoration plans as they may provide valuable ecosystem functions after a disturbance.
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Affiliation(s)
- Brianne Palmer
- Department of Biology, San Diego State University, San Diego, CA, USA.
- Department of Plant Science, University of California, Davis, Davis, CA, USA.
| | - Dawn Lawson
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - David A Lipson
- Department of Biology, San Diego State University, San Diego, CA, USA
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Miao L, Li C, Adyel TM, Huang W, Wu J, Yu Y, Hou J. Effects of the Desiccation Duration on the Dynamic Responses of Biofilm Metabolic Activities to Rewetting. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:1828-1836. [PMID: 36637413 DOI: 10.1021/acs.est.2c07410] [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] [Indexed: 06/17/2023]
Abstract
Global climate changes have increased the duration and frequency of river flow interruption, affecting the physical and community structure of benthic biofilms. However, the dynamic responses of biofilm metabolism during the dry-wet transition remain poorly understood. Herein, the dynamic changes in biofilm metabolic activities were investigated through mesocosm experiments under short-term (25 day) and long-term drought (90 day), followed by a 20 day rewetting. The biofilm ecosystem metabolism, as measured by gross primary production and community respiration, was significantly inhibited and turned heterotrophic during the desiccation phase and then recovered, becoming autotrophic during the rewetting period regardless of the desiccation periods due to the high resilience of the autotrophic community. However, long-term drought decreased the recovery rate of the ecosystem metabolism and also caused irreparable damage to the biofilm carbon metabolism, measured using Biolog Eco Plates. Specifically, the recovery of the total carbon metabolic activity is related to the specific carbon source utilized by biofilm microorganisms, such as polymers, carbohydrates, and carboxylic acids. However, the divergent changes of amino acids caused the failure of the total carbon metabolism in long-term drought treatments to recover to the control level even after 20 days of rewetting. This research provides direct evidence that the increased duration of non-flow periods affects biofilm-mediated carbon biogeochemical processes.
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Affiliation(s)
- Lingzhan Miao
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Chaoran Li
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Tanveer M Adyel
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Melbourne, Victoria 3125, Australia
| | - Wei Huang
- China Institute of Water Resources and Hydropower Research, Beijing 100038, People's Republic of China
| | - Jun Wu
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Yue Yu
- Department of Civil, Environmental, and Geomatic Engineering, ETH Zürich, Zürich 8092, Switzerland
| | - Jun Hou
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, People's Republic of China
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Abstract
This paper’s working hypothesis is that the indigenous farming practices of Timorese farmers are those most suitable and adaptable with regard to these farmers’ circumstances. Intensive farming and the acceleration of land conversion in Java lead to a reduction in favorable cropland and the degradation of soil biology. To meet the demand for food production, unfavorable areas outside Java, including marginal semi-arid areas on Timor Island, East Nusa Tenggara province, have become an important option. Unfortunately, the national crop production policy has paid less attention to the specific biophysical characteristics of the region and how local people have adapted to the diverse marginal environment. We review the literature in the areas of soil nutrition retention and soil biology, vegetation/crop diversity, and farming practices/management, including local wisdom on soil management. This paper highlights that the values of the chemical parameters of the soils in question are varied, but generally range from low to high. The existence of beneficial micro-organisms is important both for improving soil fertility and due to their association with local vegetation/crops. Traditional farming practices, such as the local agroforestry of Mamar, have effectively preserved the existence of micro-organisms that promote conservation practices, crop/vegetation diversity, and sustainable agriculture. We recommend that the expansion of croplands and crop production into marginal semi-arid areas needs to be considered and adapted while taking into consideration sustainability and environmentally sound traditional practices.
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Responses of CO2 emissions and soil microbial community structures to organic amendment in two contrasting soils in Zambia. Sci Rep 2022; 12:6368. [PMID: 35430624 PMCID: PMC9013351 DOI: 10.1038/s41598-022-10368-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 04/06/2022] [Indexed: 12/05/2022] Open
Abstract
In sub-Saharan Africa, efforts have been made to increase soil carbon (C) content in agricultural ecosystems due to severe soil degradation. The use of organic materials is a feasible method for recovering soil organic C; however, the effects of organic amendments on soil microbial communities and C cycles under C-limited soil conditions are still unknown. In this study, we conducted field experiments in Zambia using organic amendments at two sites with contrasting C content. At both sites, temporal changes in soil carbon dioxide (CO2) emissions and prokaryotic community structures were monitored during the crop growing season (126 days). The organic amendments increased CO2 emissions and prokaryotic abundance at the Kabwe site, whereas no direct impacts were observed at the Lusaka site. We also observed a larger temporal variability in the soil microbial community structure at Kabwe than that at Lusaka. These contrasting results between the two soils may be due to the microbial community stability differences between each site. However, as organic amendments have considerable potential to enhance microbial abundance and consequently sequester C at the Kabwe site, site-specific strategies are required to address the issues of soil C depletion in drylands.
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