China
Africa
Explore chapters and articles related to this topic
Advances in Microbial Molecular Biology
Published in Gustavo Molina, Zeba Usmani, Minaxi Sharma, Abdelaziz Yasri, Vijai Kumar Gupta, Microbes in Agri-Forestry Biotechnology, 2023
Deborah Catharine de Assis Leite, Naiana Cristine Gabiatti
While the traditional approaches are focused on identifying the metabolic roles of different microbes that have involved the enrichment and/or isolation of those organisms, the stable-isotope probing (SIP) is a method in which particular groups of organisms capable of incorporating specific substrates are identified without requiring cultivation. So, stable-isotope-labeled nitrogen (15N) or carbon (13C) sources may be assimilated into microbial cells from environmental samples and further separation and analysis of labeled nucleic acids (DNA-SIP or RNA-SIP) reveals functional and phylogenetic information about those microorganisms evolved in the metabolism of that given substrate (Yu et al. 2020). Neufeld et al. (2007) used 15N-DNA-SIP combined with 16S rRNA (DGGE) analysis and sequencing of picked DGGE bands. In this study, Pseudonocardia sp. is prevalent on soils treated with maize residues, while Arthrobacter sp. and Streptomyces sp. were observed in the soybean residue-treated soils. Thus, they conclude that residue quality inducing contrasting N assimilation by different bacteria groups.
Challenges of Multi-omics in Improving Microbial-assisted Phytoremediation
Published in Vivek Kumar, Rhizomicrobiome Dynamics in Bioremediation, 2021
Metaproteomics has been used to describe plant-microbe and microbe-microbe interactions in different environments. When an environment presents a low diversity, metaproteomics can provide information on the presence of proteins produced by or in presence of specific microorganisms (Delmotte et al. 2009). If combined with stable probing (e.g. metaproteomic coupled to stable isotope probing, SIP), this approach can indicate which microorganisms act in the metabolism of contaminants (Jehmlich et al. 2016). Proteomic studies can also provide information about the response of a crop to abiotic stresses, allowing the possibility to use protein markers in breeding processes (Kosová et al. 2015).
Unravelling the role of microorganisms in arsenic mobilization using metagenomic techniques
Published in Yong-Guan Zhu, Huaming Guo, Prosun Bhattacharya, Jochen Bundschuh, Arslan Ahmad, Ravi Naidu, Environmental Arsenic in a Changing World, 2019
J.R. Lloyd, E.T. Gnanaprakasam, N. Bassil, B.E. van Dongen, L.A. Richards, D.A. Polya, B.J. Mailloux, B.C. Bostick, A. van Geen
Microbial communities in the subsurface are complex, and although they may become less diverse in laboratory microcosm incubations that are designed to mimic the biogeochemical conditions that support maximal levels of arsenic mobilization, identifying the causative organisms is challenging. One approach to identify the metabolically active causative organisms is to use stable isotope probing (SIP), which can link the active fraction of a microbial community to a particular biogeochemical process. This technique has been used to identify As(V)-respiring bacteria in Cambodian aquifer sediments implicated in the reductive mobilization of arsenic (Rowland et al., 2007). 13C-labeled acetate was added to microcosm incubations, and promoted the reduction of the As(V) present in the sediments. PCR analysis of the “heavy” labeled DNA that was synthesized by the active fraction of the microbial community within the sediments (and separated from unlabeled “light” background nucleic acids by ultracentrifugation) led to the detection of known arsenate-respiring bacteria Desulfotomaculum sp. and Desulfosporosinus sp. from their characteristic 16S rRNA gene signatures. When 10 mMAs (V) was added, to enrich for As(V)-respiring bacteria, an organism closely related to the arsenate-reducing bacterium Sulfurospirillum strain NP4 was identified. This organism was also closely related to clones identified previously in West Bengal sediments associated with high arsenic concentrations. Functional gene analysis of sediments amended with 13C-labeled acetate and As (V) that targeted the As (V) respiratory reductase gene (arrA) using highly specific PCR primers, identified gene sequences most closely related to those found in S. barnesii and G. uraniireducens. Subsequent high-throughput pyrosequencing of 13C amended, heavy-labelled DNA from similar sediment incubations, have further emphasized the potential importance of organisms affiliated with known Geobacter species. Here, organisms most closely related to G. uraniireducens dominated and carried copies of the arrA As(V) respiratory reductase gene, implicated in mediating As-release in laboratory incubations.
Identification of degrader bacteria and fungi enriched in rhizosphere soil from a toluene phytoremediation site using DNA stable isotope probing
Published in International Journal of Phytoremediation, 2021
Michael BenIsrael, Jemaneh Z. Habtewold, Kamini Khosla, Philipp Wanner, Ramon Aravena, Beth L. Parker, Elizabeth A. Haack, David T. Tsao, Kari E. Dunfield
Overall, there is a motivation to broaden the collection of known degraders to improve diagnostic tools and to better understand the function and dynamics of degrader communities at impacted sites. However, study of substrate utilization by microbial communities is challenged by well-established limitations of culture-dependent techniques to study microbial communities (Stefani et al. 2015) and observed enrichment of organisms in a mixed culture cannot alone be used as conclusive evidence for active contaminant utilization (Wolicka et al. 2009). DNA stable isotope probing (DNA-SIP) is a powerful molecular technique that can reliably overcome these limitations for studying degraders by tracking utilization of a stable isotope-labeled substrate by degraders in microcosm incubations to more definitively implicate them in active biodegradation (Neufeld et al.2007). As degraders metabolize the labeled substrate, an increased fraction of the isotope label (e.g., 13C) is assimilated and used to synthesize nucleic acids. This labeled DNA (i.e., DNA with higher amounts of the label) is later isolated from unlabeled DNA via isopycnic centrifugation and characterized to target degrader organisms.
Recent biotechnological advances in petroleum hydrocarbons degradation under cold climate conditions: A review
Published in Critical Reviews in Environmental Science and Technology, 2019
Saba Miri, Mitra Naghdi, Tarek Rouissi, Satinder Kaur Brar, Richard Martel
Analysis of stable carbon isotope fractionation is another method to assess bacterial biodegradation by aerobic and anaerobic bacteria in contaminated sites (Meckenstock, Morasch, Kästner, Vieth, & Richnow, 2002). For example, C14 use demonstrated respiration in freezing temperatures such as −16 °C (Panikov & Dedysh, 2000), −4 °C (Larsen, Jonasson, & Michelsen, 2002), −2 °C (Michaelson & Ping, 2003), −18 °C (Elberling & Brandt, 2003), −39 °C (controversial) (Panikov, Flanagan, Oechel, Mastepanov, & Christensen, 2006), and in Antarctic soils up to −5 °C (Bakermans, Skidmore, Douglas, & McKay, 2014). Radiolabeled and stable isotope probing analysishave established the presence of active microorganisms in permafrost soils under frozen conditions, and they also showed that some microorganisms are capable of growth with DNA replication in permafrost soil (Altshuler et al., 2017). These methods have advantages to label the DNA of actively dividing microbes. Tuorto et al. (2014) used C13-acetate to demonstrate microbial DNA replication in permafrost soils. The active community members were part of Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, and Proteobacteria phyla. However, Firmicutes were not detected with genome replication and metabolically active, suggesting spore-forming members of this phyla in temperatures ranging from 0 °C to −20 °C (Tuorto et al., 2014).
Antibiotic resistance in agricultural soils: Source, fate, mechanism and attenuation strategy
Published in Critical Reviews in Environmental Science and Technology, 2022
Jinhua Wang, Lanjun Wang, Lusheng Zhu, Jun Wang, Baoshan Xing
Some researchers found that antibiotics degradation and ARGs variation in soil could be accelerated by enhancing microbial degradation (Wu et al., 2020). As mentioned above, the addition of biochar could change soil properties and increase the bioavailability of antibiotics, thus improving the antibiotics-degrading efficiency by microbes and attenuating ARGs (Chen, Fan, et al., 2018). Moreover, aerobic composting of antibiotics-contaminated sludge or manure indicated that increased bioactivity of antibiotics-degrading microbiota promoted the antibiotics degradation and ARGs change in soil (Urra, Alkorta, Lanzén, et al., 2019; Jang et al., 2019). Therefore, it can be seen that microbial methods are more applicable for combating antibiotic resistance in soil environments. Yang, Li, et al. (2019) isolated two antibiotic-degrading bacterial strains for penicillin V potassium (PVK) from the contaminated soil of a pig farm and the strains could be potentially used for bioremediation of PVK antibiotic-contaminated soils. In most cases, antibiotics degraders were isolated by using culture-based techniques (Topp et al., 2013), Ouyang et al. (2019) investigated sulfamethoxazole-degrading bacteria in soil microcosms by culture-independent DNA and protein stable isotope probing. The results highlighted the crucial role of yet-uncultivated indigenous bacteria for antibiotics degradation. Wu et al. (2020) constructed a tetracycline (TC)-degrading bacterial consortium containing several strains with high TC degradation efficiency, and influences generated by the introduction of the bacterial consortium on edatope were comprehensively investigated, including the evolution of soil bacterial communities, changes of soil properties, and variations in ARGs and MGEs. They reported that the soil bacterial communities and soil properties were changed and relative abundance of most ARGs and MGEs decreased after the microbial remediation (Wu et al., 2020). Hence, it seems promising to apply antibiotics-degrading bacteria or bacterial consortium for practical soil bioremediation, as it would not pose any threats to the environment (Wu et al., 2020). However, what are the end products of antibiotic biodegradation? Does the end product cause harm for soil? Therefore, the practical application of antibiotic degradation technology in soil and the harm of degradation products to soil need to be studied in the future.