1
|
Li M, Gao Y, Qian WJ, Shi L, Liu Y, Nelson WC, Nicora CD, Resch CT, Thompson C, Yan S, Fredrickson JK, Zachara JM, Liu C. Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:512-521. [PMID: 28618201 DOI: 10.1111/1758-2229.12558] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 05/31/2017] [Accepted: 06/07/2017] [Indexed: 06/07/2023]
Abstract
Microbial enzymes catalytically drive biogeochemical processes in environments. The dynamic linkage between functional enzymes and biogeochemical species transformation has, however, rarely been investigated for decades because of the challenges to directly quantify enzymes in environmental samples. The diversity of microorganisms, the low amount of available biomass and the complexity of chemical composition in environmental samples represent the main challenges. To address the diversity challenge, we first identify several signature peptides that are conserved in the targeted enzymes with the same functionality across many phylogenetically diverse microorganisms using metagenome-based protein sequence data. Quantification of the signature peptides then allows estimation of the targeted enzyme abundance. To achieve analyses of the requisite sensitivity for complex environmental samples with low available biomass, we adapted a recently developed ultrasensitive targeted quantification technology, termed high-pressure high-resolution separations with intelligent selection and multiplexing (PRISM) by improving peptide separation efficiency and method detection sensitivity. Nitrate reduction dynamics catalyzed by dissimilatory and assimilatory enzymes in a hyporheic zone sediment was used as an example to demonstrate the application of the enzyme quantification approach. Together with the measurements of biogeochemical species, the approach enables investigating the dynamic linkage between functional enzymes and biogeochemical processes.
Collapse
Affiliation(s)
- Minjing Li
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, People's Republic of China
| | - Yuqian Gao
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Wei-Jun Qian
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Liang Shi
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Yuanyuan Liu
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | | | - Carrie D Nicora
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Charles T Resch
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | | | - Sen Yan
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, People's Republic of China
| | | | - John M Zachara
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Chongxuan Liu
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, People's Republic of China
| |
Collapse
|
2
|
Saggar S, Jha N, Deslippe J, Bolan NS, Luo J, Giltrap DL, Kim DG, Zaman M, Tillman RW. Denitrification and N2O:N2 production in temperate grasslands: processes, measurements, modelling and mitigating negative impacts. THE SCIENCE OF THE TOTAL ENVIRONMENT 2013; 465:173-95. [PMID: 23260378 DOI: 10.1016/j.scitotenv.2012.11.050] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 11/11/2012] [Accepted: 11/12/2012] [Indexed: 05/02/2023]
Abstract
In this review we explore the biotic transformations of nitrogenous compounds that occur during denitrification, and the factors that influence denitrifier populations and enzyme activities, and hence, affect the production of nitrous oxide (N2O) and dinitrogen (N2) in soils. Characteristics of the genes related to denitrification are also presented. Denitrification is discussed with particular emphasis on nitrogen (N) inputs and dynamics within grasslands, and their impacts on the key soil variables and processes regulating denitrification and related gaseous N2O and N2 emissions. Factors affecting denitrification include soil N, carbon (C), pH, temperature, oxygen supply and water content. We understand that the N2O:N2 production ratio responds to the changes in these factors. Increased soil N supply, decreased soil pH, C availability and water content generally increase N2O:N2 ratio. The review also covers approaches to identify and quantify denitrification, including acetylene inhibition, (15)N tracer and direct N2 quantification techniques. We also outline the importance of emerging molecular techniques to assess gene diversity and reveal enzymes that consume N2O during denitrification and the factors affecting their activities and consider a process-based approach that can be used to quantify the N2O:N2 product ratio and N2O emissions with known levels of uncertainty in soils. Finally, we explore strategies to reduce the N2O:N2 product ratio during denitrification to mitigate N2O emissions. Future research needs to focus on evaluating the N2O-reducing ability of the denitrifiers to accelerate the conversion of N2O to N2 and the reduction of N2O:N2 ratio during denitrification.
Collapse
Affiliation(s)
- Surinder Saggar
- Ecosystems & Global Change Team, Landcare Research, Private Bag 11052, Palmerston North 4442, New Zealand.
| | | | | | | | | | | | | | | | | |
Collapse
|
3
|
Correa-Galeote D, Tortosa G, Bedmar EJ. Determination of Denitrification Genes Abundance in Environmental Samples. ACTA ACUST UNITED AC 2013. [DOI: 10.4303/mg/235702] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
4
|
|
5
|
Ji G, Tong J, Tan Y. Wastewater treatment efficiency of a multi-media biological aerated filter (MBAF) containing clinoptilolite and bioceramsite in a brick-wall embedded design. BIORESOURCE TECHNOLOGY 2011; 102:550-557. [PMID: 20797854 DOI: 10.1016/j.biortech.2010.07.075] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Revised: 07/12/2010] [Accepted: 07/18/2010] [Indexed: 05/29/2023]
Abstract
A multi-media biological aerated filter (MBAF) with clinoptilolite media was used to treat synthetic wastewater. Coal ash bioceramsite with supplemental metallic iron was added to the clinoptilolite media of MBAFs in a brick-wall embedded design. Performance parameters, such as hydraulic, organic, N and P loading capacity and microbial community composition were studied for different quantity of supplemental metallic iron contained in three MBAFs. The MBAFs with more metallic iron were found to have superior hydraulic and organic loading, and higher N and P capacities. COD, NH3-N and TP removal dropped by 7-10%, 6-7% and 4-5%, respectively, with when hydraulic loading was raised from 2.8 to 7.5 m3 m(-2) d(-1). NH3-N removal also decreased 8-9% when ammonia loading was elevated from 0.078 to 0.156 kg NH3-N m(-3) d(-1). Real-time PCR revealed a relatively stable bacterial community composed primarily of eubacteria that formed after an initial 120 d operational period. Doubling the amount of metallic iron in the bioceramsite media resulted in a twofold increase of eubacteria in the MBAF, but a decrease in the ratio of anaerobic ammonia-oxidizing bacteria to total bacteria.
Collapse
Affiliation(s)
- Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China.
| | | | | |
Collapse
|
6
|
Pierre-Alain M, Christophe M, Séverine S, Houria A, Philippe L, Lionel R. Protein extraction and fingerprinting optimization of bacterial communities in natural environment. MICROBIAL ECOLOGY 2007; 53:426-34. [PMID: 16944344 DOI: 10.1007/s00248-006-9121-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2006] [Revised: 04/28/2006] [Accepted: 05/22/2006] [Indexed: 05/11/2023]
Abstract
Recent development in molecular approaches allows access to genetic structure and diversity of indigenous microbial communities. In contrast, the functional analysis of microorganisms in their environment is still hampered by methodological limitations. Analysis of total proteins expressed at the whole community level (metaproteome) has been proposed to characterize the functional structure of microbial communities in their environment. However, developments are still required to perform such analysis. Our aim was to optimize methods to extract and characterize metaproteome of indigenous microbial communities. Experiments were first conducted in monoxenic bacterial cultures, and various methods were examined to define a procedure of protein extraction ensuring an efficient recovery regardless of the taxonomic affiliation of the cells. These developments were next applied to characterize the metaproteome from indigenous bacterial communities in freshwater samples. Bacterial cells were recovered from water using a high-speed density gradient centrifugation method before protein extraction and fingerprinting. The reactivity and sensitivity of this metaproteomic approach were tested by analyzing the variations of protein fingerprints according to perturbations (cadmium or mercury contamination). The genetic structure of the corresponding communities was also characterized by automated ribosomal spacer analysis (ARISA) DNA fingerprinting. Both protein and DNA fingerprints were statistically analyzed. Results obtained showed that the method developed for protein recovery and fingerprinting was efficient, sensitive, and reproducible. Both the functional and genetic structures of the freshwater bacterial community were complex and varied with perturbations. These variations occurred at both population and protein expression levels and were specific to the perturbation applied.
Collapse
Affiliation(s)
- Maron Pierre-Alain
- UMR Microbiologie et Géochimie des Sols, INRA/Université de Bourgogne CMSE, BP 86510, 17 rue de Sully, 21065, Dijon, Cedex, France.
| | | | | | | | | | | |
Collapse
|
7
|
Maron PA, Ranjard L, Mougel C, Lemanceau P. Metaproteomics: a new approach for studying functional microbial ecology. MICROBIAL ECOLOGY 2007; 53:486-93. [PMID: 17431707 DOI: 10.1007/s00248-006-9196-8] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2006] [Revised: 11/17/2006] [Accepted: 11/26/2006] [Indexed: 05/14/2023]
Abstract
In the postgenomic era, there is a clear recognition of the limitations of nucleic acid-based methods for getting information on functions expressed by microbial communities in situ. In this context, the large-scale study of proteins expressed by indigenous microbial communities (metaproteome) should provide information to gain insights into the functioning of the microbial component in ecosystems. Characterization of the metaproteome is expected to provide data linking genetic and functional diversity of microbial communities. Studies on the metaproteome together with those on the metagenome and the metatranscriptome will contribute to progress in our knowledge of microbial communities and their contribution in ecosystem functioning. Effectiveness of the metaproteomic approach will be improved as increasing metagenomic information is made available thanks to the environmental sequencing projects currently running. More specifically, analysis of metaproteome in contrasted environmental situations should allow (1) tracking new functional genes and metabolic pathways and (2) identifying proteins preferentially associated with specific stresses. These proteins considered as functional bioindicators should contribute, in the future, to help policy makers in defining strategies for sustainable management of our environment.
Collapse
Affiliation(s)
- Pierre-Alain Maron
- UMR Microbiologie et Géochimie des Sols, INRA/Université de Bourgogne, CMSE, BP 86510, 17 rue de Sully, 21065, Dijon Cedex, France
| | | | | | | |
Collapse
|
8
|
Philippot L, Hallin S. Finding the missing link between diversity and activity using denitrifying bacteria as a model functional community. Curr Opin Microbiol 2005; 8:234-9. [PMID: 15939345 DOI: 10.1016/j.mib.2005.04.003] [Citation(s) in RCA: 172] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2005] [Accepted: 04/12/2005] [Indexed: 11/16/2022]
Abstract
The recent development and application of numerous methods mainly based on 16S rDNA analyses have brought insights into the questions of which and how many bacterial populations can be found in a given ecosystem. A new and challenging question for microbial ecologists has emerged from the exploration of this diversity: what is its significance for ecosystem functioning? We propose the denitrifying bacteria as a model microbial community for understanding the relationship between community structure and activity, and have summarized the recent progress in studies of this functional community.
Collapse
Affiliation(s)
- Laurent Philippot
- UMR Microbiologie et Géochimie des Sols, INRA-Université de Bourgogne, CMSE, 17, rue Sully, BV 86510, 21065 Dijon Cedex, France.
| | | |
Collapse
|
9
|
Van de Pas-Schoonen KT, Schalk-Otte S, Haaijer S, Schmid M, Op den Camp H, Strous M, Gijs Kuenen J, Jetten MSM. Complete conversion of nitrate into dinitrogen gas in co-cultures of denitrifying bacteria. Biochem Soc Trans 2005; 33:205-9. [PMID: 15667308 DOI: 10.1042/bst0330205] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In the past 10 years many molecular aspects of microbial nitrate reduction have been elucidated, but the ecophysiology of this process is hardly understood. In this contribution, our efforts to study the complex microbial communities and interactions involved in the reduction of nitrate to dinitrogen gas are summarized. The initial work concentrated on emission of the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalis. As more research methods became available, the fitness of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably with the nitrate-reducing bacterium Pseudomonas G9. Finally, the advancement of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/and antibodies raised against the various NO(x) reductases. Given the enormous complexity of substrates and environmental conditions, it is evident that mixed cultures rather than single species are responsible for denitrification in man-made and natural ecosystems. However, it is surprising that even for the breakdown of a single compound, such as acetate, mixed cultures are responsible, and that the consecutive denitrification steps are commonly performed by mutualistic co-operating species. Our observations also indicate that we seldom know the identity of the major key players in the nitrogen cycle of these ecosystems.
Collapse
Affiliation(s)
- K T Van de Pas-Schoonen
- Department of Microbiology, RU Nijmegen NL, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
| | | | | | | | | | | | | | | |
Collapse
|