1
|
Chaudhury R, Chakraborty A, Rahaman F, Sarkar T, Dey S, Das M. Mycorrhization in trees: ecology, physiology, emerging technologies and beyond. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:145-156. [PMID: 38194349 DOI: 10.1111/plb.13613] [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: 07/02/2023] [Accepted: 11/30/2023] [Indexed: 01/10/2024]
Abstract
Mycorrhization has been an integral part of plants since colonization by the early land plants. Over decades, substantial research has highlighted its potential role in improving nutritional efficiency and growth, development and survival of crop plants. However, the focus of this review is trees. Evidence have been provided to explain ecological and physiological significance of mycorrhization in trees. Advances in recent technologies (e.g., metagenomics, artificial intelligence, machine learning, agricultural drones) may open new windows to apply this knowledge in promoting tree growth in forest ecosystems. Dual mycorrhization relationships in trees and even triple relationships among trees, mycorrhizal fungi and bacteria offer an interesting physiological system to understand how plants interact with other organisms for better survival. Besides, studies indicate additional roles of mycorrhization in learning, memorizing and communication between host trees through a common mycorrhizal network (CMN). Recent observations in trees suggest that mycorrhization may even promote tolerance to multiple abiotic (e.g., drought, salt, heavy metal stress) and biotic (e.g. fungi) stresses. Due to the extent of physiological reliance, local adaptation of trees is heavily impacted by the mycorrhizal community. This knowledge opens the possibility of a non-GMO avenue to promote tree growth and development. Indeed, mycorrhization could impact growth of trees in nurserys and subsequent survival of the inoculated trees in field conditions. Future studies might integrate hyperspectral imaging and drone technologies to identify tree communities that are deficient in nitrogen and spray mycorrhizal spore formulations on them.
Collapse
Affiliation(s)
- R Chaudhury
- Department of Life Sciences, Presidency University, Kolkata, India
| | - A Chakraborty
- Department of Life Sciences, Presidency University, Kolkata, India
| | - F Rahaman
- Department of Life Sciences, Presidency University, Kolkata, India
| | - T Sarkar
- Department of Life Sciences, Presidency University, Kolkata, India
| | - S Dey
- Department of Life Sciences, Presidency University, Kolkata, India
| | - M Das
- Department of Life Sciences, Presidency University, Kolkata, India
| |
Collapse
|
2
|
Alleyne A, Mason S, Vallès Y. Characterization of the Cassava Mycobiome in Symptomatic Leaf Tissues Displaying Cassava Superelongation Disease. J Fungi (Basel) 2023; 9:1130. [PMID: 38132731 PMCID: PMC10743849 DOI: 10.3390/jof9121130] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
Superelongation disease (SED) is a fungal disease that affects cassava in the Caribbean. The symptoms include the appearance of dry necrotic spots and lesions on the leaves, which may severely affect the plant yield. However, the primary causal pathogen is difficult to culture and isolate in the lab because of its slow growth and potential contamination from faster-growing organisms. In addition, the leaf symptoms can be confused with those caused by other pathogens that produce similar necrotic spots and scab-like lesions. There is also little or no information on the contribution of endophytes, if any, to disease symptoms in cassava, a plant where the disease is prevalent. Therefore, this study aimed to characterize the fungal communities in cassava associated with SED symptoms by analyzing gross fungal morphology and performing metagenomics profiling. First, several individual pathogenic fungi were isolated and cultured from diseased cassava leaf tissues from seven locations in Barbados (BB). Both culture isolation and molecular community analyses showed the presence of several other fungi in the disease microenvironment of symptomatic cassava leaves. These included Fusarium, Colletotrichum, and Alternaria species and the suspected species Elsinoë brasiliensis synonym Sphaceloma manihoticola. Additionally, a community analysis using ITS2 amplicon sequencing of 21 symptomatic leaf tissues from BB, St. Vincent and the Grenadines (SVG), Trinidad and Tobago (TT), and Jamaica (JA) revealed that the disease symptoms of superelongation may also result from the interactions of fungal communities in the mycobiome, including Elsinoë species and other fungi such as Colletotrichum, Cercospora, Alternaria, and Fusarium. Therefore, we suggest that examining the pathobiome concept in SED in the future is necessary.
Collapse
Affiliation(s)
- Angela Alleyne
- Faculty of Science and Technology, The University of the West Indies, Cave Hill Campus, Bridgetown BB11000, Barbados (Y.V.)
| | | | | |
Collapse
|
3
|
Krishnan S, DeMaere MZ, Beck D, Ostrowski M, Seymour JR, Darling AE. Rhometa: Population recombination rate estimation from metagenomic read datasets. PLoS Genet 2023; 19:e1010683. [PMID: 36972309 PMCID: PMC10079220 DOI: 10.1371/journal.pgen.1010683] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 04/06/2023] [Accepted: 02/27/2023] [Indexed: 03/29/2023] Open
Abstract
Prokaryotic evolution is influenced by the exchange of genetic information between species through a process referred to as recombination. The rate of recombination is a useful measure for the adaptive capacity of a prokaryotic population. We introduce Rhometa (https://github.com/sid-krish/Rhometa), a new software package to determine recombination rates from shotgun sequencing reads of metagenomes. It extends the composite likelihood approach for population recombination rate estimation and enables the analysis of modern short-read datasets. We evaluated Rhometa over a broad range of sequencing depths and complexities, using simulated and real experimental short-read data aligned to external reference genomes. Rhometa offers a comprehensive solution for determining population recombination rates from contemporary metagenomic read datasets. Rhometa extends the capabilities of conventional sequence-based composite likelihood population recombination rate estimators to include modern aligned metagenomic read datasets with diverse sequencing depths, thereby enabling the effective application of these techniques and their high accuracy rates to the field of metagenomics. Using simulated datasets, we show that our method performs well, with its accuracy improving with increasing numbers of genomes. Rhometa was validated on a real S. pneumoniae transformation experiment, where we show that it obtains plausible estimates of the rate of recombination. Finally, the program was also run on ocean surface water metagenomic datasets, through which we demonstrate that the program works on uncultured metagenomic datasets.
Collapse
Affiliation(s)
- Sidaswar Krishnan
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Matthew Z. DeMaere
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Sydney, NSW, Australia
- * E-mail:
| | - Dominik Beck
- Centre for Health Technologies and the School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW, Australia
| | - Martin Ostrowski
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Justin R. Seymour
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Aaron E. Darling
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Sydney, NSW, Australia
- Illumina Australia Pty Ltd, Ultimo, NSW, Australia
| |
Collapse
|
4
|
Lou D, Zhang X, Cao Y, Zhou Z, Liu C, Kuang G, Tan J, Zhu L. A novel NADP(H)-dependent 3α-HSDH from the intestinal microbiome of Ursus thibetanus. Int J Biol Macromol 2022; 219:159-165. [PMID: 35934074 DOI: 10.1016/j.ijbiomac.2022.07.252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/28/2022] [Accepted: 07/30/2022] [Indexed: 11/05/2022]
Abstract
3α-HSDHs have a crucial role in the bioconversion of steroids, and have been widely applied in the detection of total bile acid (TBA). In this study, we report a novel NADP(H)-dependent 3α-HSDH (named Sc 3α-HSDH) cloned from the intestinal microbiome of Ursus thibetanus. Sc 3α-HSDH was solubly expressed in E. coli (BL21) as a recombinant glutathione-S-transferase (GST)-tagged protein and freed from its GST-fusion by cleavage using the PreScission protease. Sc 3α-HSDH is a new member of the short-chain dehydrogenases/reductase superfamily (SDRs) with a typical α/β folding pattern, based on protein three-dimensional models predicted by AlphaFold. The best activity of Sc 3α-HSDH occurred at pH 8.5 and the temperature optima was 55 °C, indicating that Sc 3α-HSDH is not an extremozyme. The catalytic efficiencies (kcat/Km) of Sc 3α-HSDH catalyzing the oxidation reaction with the substrates, glycochenodeoxycholic acid (GCDCA) and glycoursodeoxycholic acid (GUDCA), were 183.617 and 34.458 s-1 mM-1, respectively. In addition, multiple metal ions can enhance the activity of Sc 3α-HSDH when used at concentrations ranging from 2 % to 42 %. The results also suggest that the metagenomic approach is an efficient method for identifying novel enzymes.
Collapse
Affiliation(s)
- Deshuai Lou
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological and Chemical Engineering, Chongqing University of Education, Chongqing 400067, PR China.
| | - Xiaoli Zhang
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological and Chemical Engineering, Chongqing University of Education, Chongqing 400067, PR China
| | - Yangyang Cao
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological and Chemical Engineering, Chongqing University of Education, Chongqing 400067, PR China
| | - Zixin Zhou
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological and Chemical Engineering, Chongqing University of Education, Chongqing 400067, PR China
| | - Cheng Liu
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological and Chemical Engineering, Chongqing University of Education, Chongqing 400067, PR China
| | - Gang Kuang
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological and Chemical Engineering, Chongqing University of Education, Chongqing 400067, PR China
| | - Jun Tan
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological and Chemical Engineering, Chongqing University of Education, Chongqing 400067, PR China
| | - Liancai Zhu
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, PR China.
| |
Collapse
|
5
|
Wang H, Li J, Liang X, Tao S, Wu Z, Wei G. Taxonomic and Functional Diversity of
Dendrobium Officinale
Microbiome in Danxia Habitat. J Appl Microbiol 2022; 132:3758-3770. [DOI: 10.1111/jam.15488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/08/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Huan Wang
- School of Pharmaceutical Sciences Guangzhou University of Chinese Medicine Guangzhou China
| | - Jinyan Li
- School of Pharmaceutical Sciences Guangzhou University of Chinese Medicine Guangzhou China
| | - Xiaoxia Liang
- School of Pharmaceutical Sciences Guangzhou University of Chinese Medicine Guangzhou China
| | - Shengchang Tao
- School of Pharmaceutical Sciences Guangzhou University of Chinese Medicine Guangzhou China
- Department of Pharmacy, Affiliated Dongguan People's Hospital Southern Medical University Dongguan China
| | - Zhanghua Wu
- School of Pharmaceutical Sciences Guangzhou University of Chinese Medicine Guangzhou China
- Shaoguan Institute of Danxia Dendrobium Officinale Shaoguan China
| | - Gang Wei
- School of Pharmaceutical Sciences Guangzhou University of Chinese Medicine Guangzhou China
| |
Collapse
|
6
|
Adnane M, Chapwanya A. A Review of the Diversity of the Genital Tract Microbiome and Implications for Fertility of Cattle. Animals (Basel) 2022; 12:ani12040460. [PMID: 35203168 PMCID: PMC8868056 DOI: 10.3390/ani12040460] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 01/30/2022] [Accepted: 01/31/2022] [Indexed: 12/11/2022] Open
Abstract
Cattle have a genital microbiome that is established early in life, even before calving. Microbial influx into the reproductive system of cows, during calving or mating, is unavoidable and is likely to alter the commensal microflora composition. It is now well established that a commensal endometrial flora is largely responsible for the overall fertility of cows. These microbes are important for maintenance of structural integrity of the genital mucosal barrier, immunomodulation, and protection against pathogens. Further, the genital microbiome functions in the semiochemical communication between a male and female. An optimal balance between the abundance and diversity of the microbiome is essential to promote female genital tract health. Disruption of this balance leads to dysbiosis and genital diseases and perturbed fertility. As part of the global strategy of One World, One Health, there is a need to reduce antibiotic use in animals. This area of research has the potential to expand the knowledge about the nexus between the endometrial microbiome and fertility including being probiotic in different species.
Collapse
Affiliation(s)
- Mounir Adnane
- Institute of Veterinary Sciences, University of Tiaret, Tiaret 14000, Algeria
- Correspondence: ; Tel.: +21-3542-477061
| | - Aspinas Chapwanya
- Department of Clinical Sciences, Ross University School of Veterinary Medicine, West Indies, Basseterre 00265, Saint Kitts and Nevis;
| |
Collapse
|
7
|
Mohamed SS, Abdelhamid SA, Ali RH. Isolation and identification of marine microbial products. J Genet Eng Biotechnol 2021; 19:162. [PMID: 34665351 PMCID: PMC8526645 DOI: 10.1186/s43141-021-00259-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 10/02/2021] [Indexed: 11/16/2022]
Abstract
Background The ocean is one of the world’s most important sources of bioactive chemicals in the marine environment. Microbiologists, ecologists, agronomists, taxonomists, and evolutionary biologists have been increasingly interested in marine microbial natural products (MMNPs) in recent decades. Main body Diverse marine bacteria appear to get the ability to manufacture an astounding diversity of MMNPs with a wide range of biological actions, including anti-tumor, antimicrobial, and anti-cardiovascular agents according to numerous studies. Short conclusions Innovative isolation and culture methodologies, tactics for identifying novel MMNPs via routine screens, metagenomics, genomics, combinatorial biosynthesis, and synthetic biology are all discussed in this review. There is also a discussion of potential issues and future directions for studying MMNPs.
Collapse
Affiliation(s)
- Sahar Saleh Mohamed
- Microbial Biotechnology Department, Genetic Engineering Division, National Research Centre, Cairo, Egypt
| | | | | |
Collapse
|
8
|
Herruzo-Ruiz AM, Fuentes-Almagro CA, Jiménez-Pastor JM, Pérez-Rosa VM, Blasco J, Michán C, Alhama J. Meta-omic evaluation of bacterial microbial community structure and activity for the environmental assessment of soils: overcoming protein extraction pitfalls. Environ Microbiol 2021; 23:4706-4725. [PMID: 34258847 DOI: 10.1111/1462-2920.15673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/08/2021] [Accepted: 07/11/2021] [Indexed: 11/27/2022]
Abstract
Microorganisms play unique, essential and integral roles in the biosphere. This work aims to assess the utility of soil's metaomics for environmental diagnosis. Doñana National Park (DNP) was selected as a natural lab since it contains a strictly protected core that is surrounded by numerous threats of pollution. Culture-independent high-throughput molecular tools were used to evaluate the alterations of the global structure and metabolic activities of the microbiome. 16S rRNA sequencing shows lower bacterial abundance and diversity in areas historically exposed to contamination that surround DNP. For metaproteomics, an innovative post-alkaline protein extraction protocol was developed. After NaOH treatment, successive washing with Tris-HCl buffer supplemented with glycerol was essential to eliminate interferences. Starting from soils with different physicochemical characteristics, the method renders proteins with a remarkable resolution on SDS-PAGE gels. The proteins extracted were analysed by using an in-house database constructed from the rRNA data. LC-MS/MS analysis identified 2182 non-redundant proteins with 135 showing significant differences in relative abundance in the soils around DNP. Relevant global biological processes were altered in response to the environmental changes, such as protective and antioxidant mechanisms, translation, folding and homeostasis of proteins, membrane transport and aerobic respiratory metabolism.
Collapse
Affiliation(s)
- Ana M Herruzo-Ruiz
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, Córdoba, E-14071, Spain
| | | | - José M Jiménez-Pastor
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, Córdoba, E-14071, Spain
| | - Víctor M Pérez-Rosa
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, Córdoba, E-14071, Spain
| | - Julián Blasco
- Department of Ecology and Coastal Management, ICMAN-CSIC, Campus Rio San Pedro, Puerto Real, E-11510, Spain
| | - Carmen Michán
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, Córdoba, E-14071, Spain
| | - José Alhama
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Campus de Rabanales, Edificio Severo Ochoa, Córdoba, E-14071, Spain
| |
Collapse
|
9
|
A comparative analysis of the intrauterine transcriptome in fertile and subfertile mares using cytobrush sampling. BMC Genomics 2021; 22:377. [PMID: 34022808 PMCID: PMC8141133 DOI: 10.1186/s12864-021-07701-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/11/2021] [Indexed: 12/13/2022] Open
Abstract
Background Subfertility is a major problem in modern horse breeding. Especially, mares without clinical signs of reproductive diseases, without known uterine pathogens and no evidence of inflammation but not becoming pregnant after several breeding attempts are challenging for veterinarians. To obtain new insights into the cause of these fertility problems and aiming at improving diagnosis of subfertile mares, a comparative analysis of the intrauterine transcriptome in subfertile and fertile mares was performed. Uterine cytobrush samples were collected during estrus from 57 mares without clinical signs of uterine diseases. RNA was extracted from the cytobrush samples and samples from 11 selected subfertile and 11 fertile mares were used for Illumina RNA-sequencing. Results The cytobrush sampling was a suitable technique to isolate enough RNA of high quality for transcriptome analysis. Comparing subfertile and fertile mares, 114 differentially expressed genes (FDR = 10%) were identified. Metascape enrichment analysis revealed that genes with lower mRNA levels in subfertile mares were related to ‘extracellular matrix (ECM)’, ‘ECM-receptor interaction’, ‘focal adhesion’, ‘immune response’ and ‘cytosolic calcium ion concentration’, while DEGs with higher levels in subfertile mares were enriched for ‘monocarboxyl acid transmembrane transport activity’ and ‘protein targeting’. Conclusion Our study revealed significant differences in the uterine transcriptome between fertile and subfertile mares and provides leads for potential uterine molecular biomarkers of subfertility in the mare. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07701-3.
Collapse
|
10
|
Shi Z, Zhao R, Wan J, Li B, Shen Y, Zhang S, Luo G. Metagenomic analysis reveals the fate of antibiotic resistance genes in two-stage and one-stage anaerobic digestion of waste activated sludge. JOURNAL OF HAZARDOUS MATERIALS 2021; 406:124595. [PMID: 33302189 DOI: 10.1016/j.jhazmat.2020.124595] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/20/2020] [Accepted: 11/13/2020] [Indexed: 06/12/2023]
Abstract
Waste activated sludge (WAS) from wastewater treatment plants is an important reservoir of antibiotic resistance genes (ARGs). The fate of ARGs in this process was not revealed previously. The present study applied metagenomic approach to examine the occurrence and fate of ARGs in thermophilic alkaline fermentation followed by mesophilic anaerobic digestion (TM), by comparison with mesophilic alkaline fermentation followed by mesophilic anaerobic digestion (MM) and one-stage mesophilic anaerobic digestion (M) process. The removal efficiency of two-stage anaerobic digestion (AD) to total ARGs is higher than that of one-stage AD. The hydrogen and methane production stages of two-stage AD processes have dissimilar impact on the fate of ARGs. Macrolide, lincosamide, and streptogramin (MLS) resistance genes were enriched, especially in the hydrogen production reactors of TM and MM processes. Statistical analysis of metagenomic profiles analysis suggested that bacA may be the differential ARG subtype of two-stage AD process. ARG-like sequences encoding antibiotic efflux pump, antibiotic inactivation and antibiotic target alteration mechanisms were identified as the dominant ARGs resistance mechanisms in all samples. Procrustes analysis showed that microbial community composition structured the resistome. Co-occurrence patterns between ARGs and microbial phylogeny revealed that 26 bacterial species might be potential hosts of 94 ARG subtypes.
Collapse
Affiliation(s)
- Zhijian Shi
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Renxin Zhao
- Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Jingjing Wan
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Bing Li
- Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.
| | - Yan Shen
- Huzhou Mizuda Environmental Protection Industry Research Co., Ltd, Huzhou 313000, China
| | - Shicheng Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China.
| |
Collapse
|
11
|
Chen H, Fu K, Pang B, Wang J, Li H, Jiang Z, Feng Y, Tian W, Cao R. Determination of uterine bacterial community in postpartum dairy cows with metritis based on 16S rDNA sequencing. Vet Anim Sci 2020; 10:100102. [PMID: 32734024 PMCID: PMC7386775 DOI: 10.1016/j.vas.2020.100102] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 03/13/2020] [Accepted: 03/17/2020] [Indexed: 12/29/2022] Open
Abstract
Metritis is a frequently occurring diseases in postpartum cows and is one of the important reasons for the infertility of dairy cows, accounting for 20-30% of dairy cow diseases and has serious implications for the dairy industry. It has been reported in the literature that the bacterial balance of genital tracts is directly related to the maintenance of physiological function and the development of various diseases of the reproductive system. By analyzing the changes in abundance and diversity of bacteria in the cow uterus from 1 to 35 days postpartum, the objective was to reveal the mechanism of metritis in cows and provide the basis for diagnosis, treatment and prevention of metritis in postpartum dairy cows. Uterine contents were taken from six cows (three healthy and three with metritis) on 1, 7, 14, 21 and 35 days after parturition. DNA genomes extracted from the samples were primed with 515F5'-GTGCCAGCMGCCGCGG-3' and 907R5'-CCGTCAATTCMTTRAGTTT-3' for PCR amplification of the V4+V5 regions of the 16S rDNA genes and construction of a gene library. The sequence of the bacterial structure of the cow uterine contents was analyzed using 16S rDNA high-throughput sequencing technology. A total of 30 samples were tested by PCR, and 29 samples qualified. The results of cluster analysis showed that except for one sample, the number of OTUs in the healthy cows was above 200, while in the cows with metritis, except for three samples, OTUs were below 200. The Chao1 and Shannon indices showed that the abundance of bacteria in the cow uterus was lower than that of healthy cows. Analysis of the relative abundance of bacteria in the cow uterus showed that there were six phyla present, including Bacteroidetes, Firmicutes, Fusobacteria, Proteobacteria, Actinobacteria and Tenericutes. There were 10 dominant genera in healthy cows, including Bacteroides, Clostridium sensu stricto 1, Escherichia-Shigella, Fusobacterium, Halomonas, Helcococcus, Porphyromonas, Prevotella 6, Rikenellaceae RC9 gut group and Streptococcus. There were nine dominant genera in cows with metritis, including Bacteroides, Caviibacter, Clostridium sensu stricto 1, Falsiporphyromonas, Fusobacterium, Halomonas, Helcococcus, Porphyromonas and Prevotella 7. Phylogenetic tree analysis showed that uterine contents from 29 samples could be separated into two clusters. Eleven samples from the cows with metritis were clustered with one sample from the healthy group, and 13 samples from the healthy cows were clustered together with four samples from the metritis group. Principal co-ordinate analysis showed that the points representing healthy cows and those representing the metritis group were concentrated in two distinct regions, which shows that there were significant differences in the structure evolution between healthy cows and cows with metritis. The above results indicate that bacterial diversity declines with time postpartum in healthy cows and is lower in cows with metritis, with characteristic changes in the relative abundances, including increases in Bacteroidetes and Fusobacteria, decreases in Firmicutes and Proteobacteria, increases in Porphyromonas, Bacteroides and Fusobacterium, and a decrease in Clostridium sensu stricto 1.
Collapse
Affiliation(s)
- Hao Chen
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province 266109, China
| | - Kaiqiang Fu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province 266109, China
| | - Binbin Pang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province 266109, China
| | - Jifang Wang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province 266109, China
| | - Huatao Li
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province 266109, China
| | - Zhongling Jiang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province 266109, China
| | - Yanni Feng
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province 266109, China
| | - Wenru Tian
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province 266109, China
| | - Rongfeng Cao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province 266109, China
| |
Collapse
|
12
|
Qiu J, Zhang Y, Shi Y, Jiang J, Wu S, Li L, Shao Y, Xin Z. Identification and characterization of a novel phthalate-degrading hydrolase from a soil metagenomic library. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 190:110148. [PMID: 31911388 DOI: 10.1016/j.ecoenv.2019.110148] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 12/27/2019] [Accepted: 12/28/2019] [Indexed: 06/10/2023]
Abstract
Phthalate esters have raised public concerns owing to their effects on the environment and human health. We identified a novel phthalate-degrading hydrolase, EstJ6, from a metagenomic library using function-driven screening. Phylogenetic analysis indicated that EstJ6 is a member of family IV esterases. EstJ6 hydrolyzed various dialkyl and monoalkyl phthalate esters, and exhibited high hydrolytic activity (128 U/mg) toward dibutyl phthalate at 40 °C and pH 7.5. EstJ6 hydrolyzed not only common phthalate esters with simple side chains but also diethylhexyl phthalate and monoethylhexyl phthalate, which have complex and long side chains. Site-directed mutagenesis indicated that the catalytic triad residues of EstJ6 consists of Ser146, Glu240, and His270. EstJ6 is therefore a promising biodegradation enzyme, and our study illustrates the advantages of a metagenomic approach in identifying enzyme-coding genes for agricultural, food, and biotechnological applications.
Collapse
Affiliation(s)
- Jiarong Qiu
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Yueqi Zhang
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Yaning Shi
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Junwei Jiang
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Shenglu Wu
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Longxiang Li
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Yuting Shao
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Zhihong Xin
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China.
| |
Collapse
|
13
|
Ngara TR, Zhang H. Recent Advances in Function-based Metagenomic Screening. GENOMICS PROTEOMICS & BIOINFORMATICS 2018; 16:405-415. [PMID: 30597257 PMCID: PMC6411959 DOI: 10.1016/j.gpb.2018.01.002] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/05/2018] [Accepted: 01/09/2018] [Indexed: 12/01/2022]
Abstract
Metagenomes from uncultured microorganisms are rich resources for novel enzyme genes. The methods used to screen the metagenomic libraries fall into two categories, which are based on sequence or function of the enzymes. The sequence-based approaches rely on the known sequences of the target gene families. In contrast, the function-based approaches do not involve the incorporation of metagenomic sequencing data and, therefore, may lead to the discovery of novel gene sequences with desired functions. In this review, we discuss the function-based screening strategies that have been used in the identification of enzymes from metagenomes. Because of its simplicity, agar plate screening is most commonly used in the identification of novel enzymes with diverse functions. Other screening methods with higher sensitivity are also employed, such as microtiter plate screening. Furthermore, several ultra-high-throughput methods were developed to deal with large metagenomic libraries. Among these are the FACS-based screening, droplet-based screening, and the in vivo reporter-based screening methods. The application of these novel screening strategies has increased the chance for the discovery of novel enzyme genes.
Collapse
Affiliation(s)
- Tanyaradzwa Rodgers Ngara
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, MOE Key Laboratory of Molecular Biophysics, Wuhan 430074, China
| | - Houjin Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, MOE Key Laboratory of Molecular Biophysics, Wuhan 430074, China.
| |
Collapse
|
14
|
Pathak RK, Baunthiyal M, Pandey D, Kumar A. Augmentation of crop productivity through interventions of omics technologies in India: challenges and opportunities. 3 Biotech 2018; 8:454. [PMID: 30370195 PMCID: PMC6195494 DOI: 10.1007/s13205-018-1473-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 10/09/2018] [Indexed: 01/19/2023] Open
Abstract
With the continuous increase in the population of developing countries and decline of natural resources, there is an urgent need to qualitatively and quantitatively augment crop productivity by using new tools and technologies for improvement of agriculturally important traits. The new scientific and technological omics-based approaches have enabled us to deal with several issues and challenges faced by modern agricultural system and provided us novel opportunities for ensuring food and nutritional security. Recent developments in sequencing techniques have made available huge amount of genomic and transcriptomic data on model and cultivated crop plants including Arabidopsis thaliana, Oryza sativa, Triticum aestivum etc. The sequencing data along with other data generated through several omics platforms have significantly influenced the disciplines of crop sciences. Gene discovery and expression profiling-based technologies are offering enormous opportunities to the scientific community which can now apply marker-assisted selection technology to assess and enhance diversity in their collected germplasm, introgress essential traits from new sources and investigate genes that control key traits of crop plants. Utilization of omics science and technologies for crop productivity, protection and management has recently been receiving a lot of attention; the majority of the efforts have been put into signifying the possible applications of various omics technologies in crop plant sciences. This article highlights the background of challenges and opportunities for augmentation of crop productivity through interventions of omics technologies in India.
Collapse
Affiliation(s)
- Rajesh Kumar Pathak
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
- Department of Biotechnology, G. B. Pant Institute of Engineering and Technology, Pauri Garhwal, Uttarakhand 246194 India
| | - Mamta Baunthiyal
- Department of Biotechnology, G. B. Pant Institute of Engineering and Technology, Pauri Garhwal, Uttarakhand 246194 India
| | - Dinesh Pandey
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Anil Kumar
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
- Present Address: Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh 284003 India
| |
Collapse
|
15
|
Ferrandi EE, Sayer C, De Rose SA, Guazzelli E, Marchesi C, Saneei V, Isupov MN, Littlechild JA, Monti D. New Thermophilic α/β Class Epoxide Hydrolases Found in Metagenomes From Hot Environments. Front Bioeng Biotechnol 2018; 6:144. [PMID: 30386778 PMCID: PMC6198070 DOI: 10.3389/fbioe.2018.00144] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 09/21/2018] [Indexed: 12/21/2022] Open
Abstract
Two novel epoxide hydrolases (EHs), Sibe-EH and CH65-EH, were identified in the metagenomes of samples collected in hot springs in Russia and China, respectively. The two α/β hydrolase superfamily fold enzymes were cloned, over-expressed in Escherichia coli, purified and characterized. The new EHs were active toward a broad range of substrates, and in particular, Sibe-EH was excellent in the desymmetrization of cis-2,3-epoxybutane producing the (2R,3R)-diol product with ee exceeding 99%. Interestingly these enzymes also hydrolyse (4R)-limonene-1,2-epoxide with Sibe-EH being specific for the trans isomer. The Sibe-EH is a monomer in solution whereas the CH65-EH is a dimer. Both enzymes showed high melting temperatures with the CH65-EH being the highest at 85°C retaining 80% of its initial activity after 3 h thermal treatment at 70°C making it the most thermal tolerant wild type epoxide hydrolase described. The Sibe-EH and CH65-EH have been crystallized and their structures determined to high resolution, 1.6 and 1.4 Å, respectively. The CH65-EH enzyme forms a dimer via its cap domains with different relative orientation of the monomers compared to previously described EHs. The entrance to the active site cavity is located in a different position in CH65-EH and Sibe-EH in relation to other known bacterial and mammalian EHs.
Collapse
Affiliation(s)
| | - Christopher Sayer
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Simone Antonio De Rose
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Elisa Guazzelli
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Milan, Italy
| | - Carlotta Marchesi
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Milan, Italy
| | - Vahid Saneei
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Michail N Isupov
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Jennifer A Littlechild
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Daniela Monti
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Milan, Italy
| |
Collapse
|
16
|
Westmann CA, Alves LDF, Silva-Rocha R, Guazzaroni ME. Mining Novel Constitutive Promoter Elements in Soil Metagenomic Libraries in Escherichia coli. Front Microbiol 2018; 9:1344. [PMID: 29973927 PMCID: PMC6019500 DOI: 10.3389/fmicb.2018.01344] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 05/31/2018] [Indexed: 11/13/2022] Open
Abstract
Although functional metagenomics has been widely employed for the discovery of genes relevant to biotechnology and biomedicine, its potential for assessing the diversity of transcriptional regulatory elements of microbial communities has remained poorly explored. Here, we experimentally mined novel constitutive promoter sequences in metagenomic libraries by combining a bi-directional reporter vector, high-throughput fluorescence assays and predictive computational methods. Through the expression profiling of fluorescent clones from two independent soil sample libraries, we have analyzed the regulatory dynamics of 260 clones with candidate promoters as a set of active metagenomic promoters in the host Escherichia coli. Through an in-depth analysis of selected clones, we were able to further explore the architecture of metagenomic fragments and to report the presence of multiple promoters per fragment with a dominant promoter driving the expression profile. These approaches resulted in the identification of 33 novel active promoters from metagenomic DNA originated from very diverse phylogenetic groups. The in silico and in vivo analysis of these individual promoters allowed the generation of a constitutive promoter consensus for exogenous sequences recognizable by E. coli in metagenomic studies. The results presented here demonstrates the potential of functional metagenomics for exploring environmental bacterial communities as a source of novel regulatory genetic parts to expand the toolbox for microbial engineering.
Collapse
Affiliation(s)
- Cauã A Westmann
- Department of Cellular and Molecular Biology, FMRP, University of São Paulo, Ribeirão Preto, Brazil
| | - Luana de Fátima Alves
- Department of Biology, FFCLRP, University of São Paulo, Ribeirão Preto, Brazil.,Department of Biochemistry, FMRP, University of São Paulo, Ribeirão Preto, Brazil
| | - Rafael Silva-Rocha
- Department of Cellular and Molecular Biology, FMRP, University of São Paulo, Ribeirão Preto, Brazil
| | | |
Collapse
|
17
|
Balech B, Sandionigi A, Manzari C, Trucchi E, Tullo A, Licciulli F, Grillo G, Sbisà E, De Felici S, Saccone C, D'Erchia AM, Cesaroni D, Casiraghi M, Vicario S. Tackling critical parameters in metazoan meta-barcoding experiments: a preliminary study based on coxI DNA barcode. PeerJ 2018; 6:e4845. [PMID: 29915686 PMCID: PMC6004112 DOI: 10.7717/peerj.4845] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 05/04/2018] [Indexed: 11/21/2022] Open
Abstract
Nowadays DNA meta-barcoding is a powerful instrument capable of quickly discovering the biodiversity of an environmental sample by integrating the DNA barcoding approach with High Throughput Sequencing technologies. It mainly consists of the parallel reading of informative genomic fragment/s able to discriminate living entities. Although this approach has been widely studied, it still needs optimization in some necessary steps requested in its advanced accomplishment. A fundamental element concerns the standardization of bioinformatic analyses pipelines. The aim of the present study was to underline a number of critical parameters of laboratory material preparation and taxonomic assignment pipelines in DNA meta-barcoding experiments using the cytochrome oxidase subunit-I (coxI) barcode region, known as a suitable molecular marker for animal species identification. We compared nine taxonomic assignment pipelines, including a custom in-house method, based on Hidden Markov Models. Moreover, we evaluated the potential influence of universal primers amplification bias in qPCR, as well as the correlation between GC content with taxonomic assignment results. The pipelines were tested on a community of known terrestrial invertebrates collected by pitfall traps from a chestnut forest in Italy. Although the present analysis was not exhaustive and needs additional investigation, our results suggest some potential improvements in laboratory material preparation and the introduction of additional parameters in taxonomic assignment pipelines. These include the correct setup of OTU clustering threshold, the calibration of GC content affecting sequencing quality and taxonomic classification, as well as the evaluation of PCR primers amplification bias on the final biodiversity pattern. Thus, careful attention and further validation/optimization of the above-mentioned variables would be required in a DNA meta-barcoding experimental routine.
Collapse
Affiliation(s)
- Bachir Balech
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari-Consiglio Nazionale delle Ricerche, Bari, Italy.,Dipartimento di Biologia, Università degli studi di Bari 'Aldo Moro', Bari, Italy
| | - Anna Sandionigi
- Dipartimento di Biotecnologie e Bioscienze-Zooplantlab, Università degli studi di Milano Bicocca, Milan, Italy
| | - Caterina Manzari
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari-Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Emiliano Trucchi
- Dipartimento di Biologia, Università di Roma Tor Vergata, Rome, Italy
| | - Apollonia Tullo
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari-Consiglio Nazionale delle Ricerche, Bari, Italy.,Istituto di Tecnologie Biomediche-Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Flavio Licciulli
- Istituto di Tecnologie Biomediche-Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Giorgio Grillo
- Istituto di Tecnologie Biomediche-Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Elisabetta Sbisà
- Istituto di Tecnologie Biomediche-Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Stefano De Felici
- Dipartimento di Biologia, Università di Roma Tor Vergata, Rome, Italy.,Istituto di Biologia Agroambientale e Forestale-Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Cecilia Saccone
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari 'Aldo Moro', Bari, Italy
| | - Anna Maria D'Erchia
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari 'Aldo Moro', Bari, Italy
| | | | - Maurizio Casiraghi
- Dipartimento di Biotecnologie e Bioscienze-Zooplantlab, Università degli studi di Milano Bicocca, Milan, Italy
| | - Saverio Vicario
- Istituto sull'Inquinamento Atmosferico-Consiglio Nazionale delle Ricerche, Bari, Italy
| |
Collapse
|
18
|
Ahmed V, Verma MK, Gupta S, Mandhan V, Chauhan NS. Metagenomic Profiling of Soil Microbes to Mine Salt Stress Tolerance Genes. Front Microbiol 2018; 9:159. [PMID: 29472909 PMCID: PMC5809485 DOI: 10.3389/fmicb.2018.00159] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/23/2018] [Indexed: 12/11/2022] Open
Abstract
Osmotolerance is one of the critical factors for successful survival and colonization of microbes in saline environments. Nonetheless, information about these osmotolerance mechanisms is still inadequate. Exploration of the saline soil microbiome for its community structure and novel genetic elements is likely to provide information on the mechanisms involved in osmoadaptation. The present study explores the saline soil microbiome for its native structure and novel genetic elements involved in osmoadaptation. 16S rRNA gene sequence analysis has indicated the dominance of halophilic/halotolerant phylotypes affiliated to Proteobacteria, Actinobacteria, Gemmatimonadetes, Bacteroidetes, Firmicutes, and Acidobacteria. A functional metagenomics approach led to the identification of osmotolerant clones SSR1, SSR4, SSR6, SSR2 harboring BCAA_ABCtp, GSDH, STK_Pknb, and duf3445 genes. Furthermore, transposon mutagenesis, genetic, physiological and functional studies in close association has confirmed the role of these genes in osmotolerance. Enhancement in host osmotolerance possibly though the cytosolic accumulation of amino acids, reducing equivalents and osmolytes involving BCAA-ABCtp, GSDH, and STKc_PknB. Decoding of the genetic elements prevalent within these microbes can be exploited either as such for ameliorating soils or their genetically modified forms can assist crops to resist and survive in saline environment.
Collapse
Affiliation(s)
- Vasim Ahmed
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Manoj K Verma
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Shashank Gupta
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Vibha Mandhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Nar S Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| |
Collapse
|
19
|
Functional metagenomics identifies novel genes ABCTPP, TMSRP1 and TLSRP1 among human gut enterotypes. Sci Rep 2018; 8:1397. [PMID: 29362424 PMCID: PMC5780487 DOI: 10.1038/s41598-018-19862-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 01/09/2018] [Indexed: 01/08/2023] Open
Abstract
Every niche in the biosphere is touched by the seemingly endless capacity of microbes to transform the world around them by adapting swiftly and flexibly to the environmental changes, likewise the gastrointestinal tract is no exception. The ability to cope with rapid changes in external osmolarity is an important aspect of gut microbes for their survival and colonization. Identification of these survival mechanisms is a pivotal step towards understanding genomic suitability of a symbiont for successful human gut colonization. Here we highlight our recent work applying functional metagenomics to study human gut microbiome to identify candidate genes responsible for the salt stress tolerance. A plasmid borne metagenomic library of Bacteroidetes enriched human fecal metagenomic DNA led to identification of unique salt osmotolerance clones SR6 and SR7. Subsequent gene analysis combined with functional studies revealed that TLSRP1 within pSR7 and TMSRP1 and ABCTPP of pSR6 are the active loci responsible for osmotolerance through an energy dependent mechanism. Our study elucidates the novel genetic machinery involved in bestowing osmotolerance in Prevotella and Bacteroidetes, the predominant microbial groups in a North Indian population. This study unravels an alternative method for imparting ionic stress tolerance, which may be prevalent in the human gut microbiome.
Collapse
|
20
|
Mahapatra DM, Joshi NV, Ramachandra TV. Insights to bioprocess and treatment competence of urban wetlands. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 206:1179-1191. [PMID: 29183650 DOI: 10.1016/j.jenvman.2017.10.054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 10/16/2017] [Accepted: 10/23/2017] [Indexed: 06/07/2023]
Abstract
Wetlands play a major role in the recharge of groundwater resources, maintenance of water quality (remediation), moderate microclimate while supporting local livelihood through provision of fish, fodder, etc. The present study aims to investigate algal-bacterial consortium as a function of residence time with the water quality dynamics in two major wetlands in Bangalore city, India. Over thirty-two genera of algae were recorded with more than 40 species in the lakes and two dominant bacterial assemblages. The higher Ammonium-N content favoured the growth of these members. Significant correlation was observed between the nutrient concentrations and the community structure at the inflows and the outflows. The algal community showed negative correlation to filterable COD and high nutrients levels while bacterial abundance was observed under high loadings. The green algae Chlorophyceae (Chlorella blooms), which are indicators of nutrient enrichment were observed predominantly, that needs an immediate attention. Higher overall treatment efficiency was observed in terms of CNP removal during the Pre-monsoon season attributed to absence of macrophytes cover and rapid growth of algal assemblage's due to higher temperature regimes with adequate solar insolation.
Collapse
Affiliation(s)
- Durga Madhab Mahapatra
- Biological and Ecological Engineering (BEE), Oregon State University, Corvallis, OR, United States; Energy and Wetlands Research Group (EWRG), Center for Ecological Sciences (CES), Indian Institute of Science, Bangalore, India; Centre for Sustainable Technologies (CST), Indian Institute of Science (IISc), Bangalore, India
| | - N V Joshi
- Energy and Wetlands Research Group (EWRG), Center for Ecological Sciences (CES), Indian Institute of Science, Bangalore, India
| | - T V Ramachandra
- Energy and Wetlands Research Group (EWRG), Center for Ecological Sciences (CES), Indian Institute of Science, Bangalore, India; Centre for Sustainable Technologies (CST), Indian Institute of Science (IISc), Bangalore, India; Centre for Infrastructure, Sustainable Transportation and Urban Planning (CiSTUP), IISc, Bangalore, India.
| |
Collapse
|
21
|
Marks PC, Bigler M, Alsop EB, Vigneron A, Lomans BP, De Paula R, Geissler B, Tsesmetzis N. MetaHCR: a web-enabled metagenome data management system for hydrocarbon resources. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:1-10. [PMID: 30212909 PMCID: PMC6146120 DOI: 10.1093/database/bay087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 07/24/2018] [Indexed: 11/16/2022]
Abstract
The ever-increasing metagenomic data necessitate appropriate cataloguing in a way that facilitates the comparison and better contextualization of the underlying investigations. To this extent, information associated with the sequencing data as well as the original sample and the environment where it was obtained from is crucial. To date, there are not any publicly available repositories able to capture environmental metadata pertaining to hydrocarbon-rich environments. As such, contextualization and comparative analysis among sequencing datasets derived from these environments is to a certain degree hindered or cannot be fully evaluated. The metagenomics data management system for hydrocarbon resources (MetaHCRs) enables the capturing of marker gene and whole metagenome sequencing data as well as over 300 contextual attributes associated with samples, organisms, environments and geological properties, among others. Moreover, MetaHCR implements the Minimum Information about any Sequence–hydrocarbon resource specification from the Genomic Standards Consortium; it integrates a user-friendly web interface and relational database model, and it enables the generation of complex custom search. MetaHCR has been tested with 36 publicly available metagenomic studies, and its modular architecture can be easily customized for other types of environmental and metagenomics studies.
Collapse
Affiliation(s)
- Peter C Marks
- Shell International Exploration and Production Inc., Houston, USA
| | - Marc Bigler
- Ecole Supérieure de Biotechnologie Strasbourg, Illkirch-Graffenstaden, France
| | - Eric B Alsop
- Shell International Exploration and Production Inc., Houston, USA.,DOE Joint Genome Institute,Walnut Creek, California, USA
| | - Adrien Vigneron
- Shell International Exploration and Production Inc., Houston, USA.,School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Bart P Lomans
- Shell Global Solutions International B.V., HW Amsterdam, Netherlands
| | | | - Brett Geissler
- RD & E Microbiology Group, NALCO Champion, Sugar Land, USA
| | - Nicolas Tsesmetzis
- Shell International Exploration and Production Inc., Houston, USA.,School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| |
Collapse
|
22
|
Characterization of the cervical bacterial community in dairy cows with metritis and during different physiological phases. Theriogenology 2017; 108:306-313. [PMID: 29284157 DOI: 10.1016/j.theriogenology.2017.12.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 12/11/2017] [Accepted: 12/13/2017] [Indexed: 01/01/2023]
Abstract
For the development of disease prevention and intervention strategies, a better understanding of the dynamics and interactions within cervical bacterial communities in both healthy cows and cows with metritis is required. Understanding the complexity and ecology of microorganisms in the vagina of dairy cows with metritis and during different physiological phases is critical for developing strategies to balance microorganism content. To gain deeper insight into fluctuations within the cervical microbiota, swab samples were collected from 40 Holstein dairy cows, and16S rDNA amplicon sequencing was used to analyze cervical bacterial diversity. Meanwhile, vaginal bacterial composition was analyzed during different physiological phases, including the formative (CF), gestational (CG), and postpartum (CP) stages, and in cows with metritis (CM). The results revealed a complex profile with extensive differences in the cervical bacterial composition. A total of 678,043clean 16S rDNA V4-V6 reads were gained, and 1877 Operational Taxonomic Units (OTUs) were observed after calculation. At both the phylum and genus levels, the top 10 bacteria by percentage were the same when comparing the CF, CG, and CP groups of cows, with some variation in abundance. At the phylum level, the cervical microbial community in the CF, CG, and CP groups included mainly Firmicutes, which accounted for 39.3%, 48.3%, and 49.6% of the total microbial composition of each group, respectively. However, the cervical bacterial community in the CM group consisted of mostly Bacteroidetes, which accounted for 72.6% of the total microbial composition. The second major bacterial community in the CF and CG groups of cows was Proteobacteria, which accounted for 28.3%and 30.1% of the total microbial compositions of these groups, respectively, while the second major bacterial community in the CP group was Bacteroidetes (23.5%). However, in the CM group, the second major bacterial community was Fusobacteria, which accounted for18.0% of the total microbial composition. At the genus level, the cervical bacterial community in the CM group of cows was dominated by Porphyromonas(44.4%) and Fusobacterium(12.1%), while Porphyromonas accounted for only 1.3%, 1.1%, and 1.4% of the total microbial compositions of the CF, CG, and CP groups, respectively. Likewise, Fusobacterium accounted for 2.3%, 0.7%, and 4.7% of the total microbial compositions of the CF, CG, and CP groups, respectively. The results demonstrate that cervical bacterial diversity decreases in cows with metritis and that the predominant bacterial genera are Porphyromonas and Fusobacterium. Cervical bacterial diversity was rich in all observed physiological phases, and the predominant bacterial phylum was Firmicutes. Pregnancy had little effect on the cervical bacterial community; however, there were increases in the abundances of pathogenic species in postpartum cows. Cervical bacterial diversity decreased in cows with metritis, however, due to the highly dynamic and complex course of metritis, the relationship between cervical bacterial diversity and metritis requires further investigation.
Collapse
|
23
|
Marzano M, Fosso B, Manzari C, Grieco F, Intranuovo M, Cozzi G, Mulè G, Scioscia G, Valiente G, Tullo A, Sbisà E, Pesole G, Santamaria M. Complexity and Dynamics of the Winemaking Bacterial Communities in Berries, Musts, and Wines from Apulian Grape Cultivars through Time and Space. PLoS One 2016; 11:e0157383. [PMID: 27299312 PMCID: PMC4907434 DOI: 10.1371/journal.pone.0157383] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 05/27/2016] [Indexed: 11/19/2022] Open
Abstract
Currently, there is very little information available regarding the microbiome associated with the wine production chain. Here, we used an amplicon sequencing approach based on high-throughput sequencing (HTS) to obtain a comprehensive assessment of the bacterial community associated with the production of three Apulian red wines, from grape to final product. The relationships among grape variety, the microbial community, and fermentation was investigated. Moreover, the winery microbiota was evaluated compared to the autochthonous species in vineyards that persist until the end of the winemaking process. The analysis highlighted the remarkable dynamics within the microbial communities during fermentation. A common microbial core shared among the examined wine varieties was observed, and the unique taxonomic signature of each wine appellation was revealed. New species belonging to the genus Halomonas were also reported. This study demonstrates the potential of this metagenomic approach, supported by optimized protocols, for identifying the biodiversity of the wine supply chain. The developed experimental pipeline offers new prospects for other research fields in which a comprehensive view of microbial community complexity and dynamics is desirable.
Collapse
Affiliation(s)
| | - Bruno Fosso
- Institute of Biomembranes and Bioenergetics, CNR, Bari, Italy
| | | | - Francesco Grieco
- Institute of Sciences of Food Production, CNR, Operative Unit of Lecce, Lecce (Le), Italy
| | - Marianna Intranuovo
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro” Bari, Italy
| | - Giuseppe Cozzi
- Institute of Sciences of Food Production, CNR, Bari, Italy
| | | | | | - Gabriel Valiente
- Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Polytechnic University of Catalonia, Barcelona, Spain
| | | | | | - Graziano Pesole
- Institute of Biomembranes and Bioenergetics, CNR, Bari, Italy
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro” Bari, Italy
- * E-mail: (MS); (GP)
| | - Monica Santamaria
- Institute of Biomembranes and Bioenergetics, CNR, Bari, Italy
- * E-mail: (MS); (GP)
| |
Collapse
|
24
|
Jordaan K, Bezuidenhout CC. Bacterial community composition of an urban river in the North West Province, South Africa, in relation to physico-chemical water quality. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:5868-5880. [PMID: 26593724 DOI: 10.1007/s11356-015-5786-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/09/2015] [Indexed: 06/05/2023]
Abstract
The aim of this study was to determine the impacts of anthropogenic disturbances on bacterial community composition in an urban river (Mooi River). Physico-chemical analysis, bacterial enumeration and 454-pyrosequencing were conducted on the Mooi River system upstream and downstream of an urban settlement in the North West Province, South Africa. Pyrosequencing and multivariate analysis showed that nutrient inputs and faecal pollution strongly impacted the physico-chemical and microbiological quality at the downstream sites. Also, bacterial communities showed higher richness and evenness at the downstream sites. Multivariate analysis suggested that the abundances of Betaproteobacteria, Epsilonproteobacteria, Acidobacteria, Bacteroidetes and Verrucomicrobia are related to temperature, pH, dissolved oxygen (DO), sulphate and chlorophyll-a levels. These results suggest that urbanisation caused the overall water quality of this river to deteriorate, which in turn affected the bacterial community composition. In addition, our work identified potential indicator groups that may be used to track faecal and organic pollution in freshwater systems.
Collapse
Affiliation(s)
- K Jordaan
- Unit for Environmental Science and Management, North-West University, Potchefstroom Campus, Private Bag X6001, Potchefstroom, 2520, South Africa
| | - C C Bezuidenhout
- Unit for Environmental Science and Management, North-West University, Potchefstroom Campus, Private Bag X6001, Potchefstroom, 2520, South Africa.
| |
Collapse
|
25
|
Laguardia-Nascimento M, Branco KMGR, Gasparini MR, Giannattasio-Ferraz S, Leite LR, Araujo FMG, Salim ACDM, Nicoli JR, de Oliveira GC, Barbosa-Stancioli EF. Vaginal Microbiome Characterization of Nellore Cattle Using Metagenomic Analysis. PLoS One 2015; 10:e0143294. [PMID: 26599789 PMCID: PMC4657983 DOI: 10.1371/journal.pone.0143294] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/03/2015] [Indexed: 12/24/2022] Open
Abstract
Understanding of microbial communities inhabiting cattle vaginal tract may lead to a better comprehension of bovine physiology and reproductive health being of great economic interest. Up to date, studies involving cattle microbiota are focused on the gastrointestinal tract, and little is known about the vaginal microbiota. This study aimed to investigate the vaginal microbiome in Nellore cattle, heifers and cows, pregnant and non-pregnant, using a culture independent approach. The main bacterial phyla found were Firmicutes (~40–50%), Bacteroidetes (~15–25%) and Proteobacteria (~5–25%), in addition to ~10–20% of non-classified bacteria. 45–55% of the samples were represented by only ten OTUs: Aeribacillus, Bacteroides, Clostridium, Ruminococcus, Rikenella, Alistipes, Bacillus, Eubacterium, Prevotella and non-classified bacteria. Interestingly, microbiota from all 20 animals could be grouped according to the respiratory metabolism of the main OTUs found, creating three groups of vaginal microbiota in cattle. Archaeal samples were dominated by the Methanobrevibacter genus (Euryarchaeota, ~55–70%). Ascomycota was the main fungal phylum (~80–95%) and Mycosphaerella the most abundant genus (~70–85%). Hormonal influence was not clear, but a tendency for the reduction of bacterial and increase of archaeal populations in pregnant animals was observed. Eukaryotes did not vary significantly between pregnant and non-pregnant animals, but tended to be more abundant on cows than on heifers. The present work describes a great microbial variability in the vaginal community among the evaluated animals and groups (heifers and cows, pregnant and non-pregnant), which is significantly different from the findings previously reported using culture dependent methods, pointing out the need for further studies on this issue. The microbiome found also indicates that the vaginal colonization appears to be influenced by the gastrointestinal community.
Collapse
Affiliation(s)
- Mateus Laguardia-Nascimento
- Departmento de Microbiologia, Instituto de Ciencias Biologicas, Universidade Federal Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Marcela Ribeiro Gasparini
- Departmento de Microbiologia, Instituto de Ciencias Biologicas, Universidade Federal Minas Gerais, Belo Horizonte, MG, Brazil
| | - Silvia Giannattasio-Ferraz
- Departmento de Microbiologia, Instituto de Ciencias Biologicas, Universidade Federal Minas Gerais, Belo Horizonte, MG, Brazil
| | | | | | | | - Jacques Robert Nicoli
- Departmento de Microbiologia, Instituto de Ciencias Biologicas, Universidade Federal Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Edel Figueiredo Barbosa-Stancioli
- Departmento de Microbiologia, Instituto de Ciencias Biologicas, Universidade Federal Minas Gerais, Belo Horizonte, MG, Brazil
- * E-mail:
| |
Collapse
|
26
|
Ferrandi EE, Sayer C, Isupov MN, Annovazzi C, Marchesi C, Iacobone G, Peng X, Bonch-Osmolovskaya E, Wohlgemuth R, Littlechild JA, Monti D. Discovery and characterization of thermophilic limonene-1,2-epoxide hydrolases from hot spring metagenomic libraries. FEBS J 2015; 282:2879-94. [PMID: 26032250 DOI: 10.1111/febs.13328] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/20/2015] [Accepted: 05/26/2015] [Indexed: 11/28/2022]
Abstract
The epoxide hydrolases (EHs) represent an attractive option for the synthesis of chiral epoxides and 1,2-diols which are valuable building blocks for the synthesis of several pharmaceutical compounds. A metagenomic approach has been used to identify two new members of the atypical EH limonene-1,2-epoxide hydrolase (LEH) family of enzymes. These two LEHs (Tomsk-LEH and CH55-LEH) show EH activities towards different epoxide substrates, differing in most cases from those previously identified for Rhodococcus erythropolis (Re-LEH) in terms of stereoselectivity. Tomsk-LEH and CH55-LEH, both from thermophilic sources, have higher optimal temperatures and apparent melting temperatures than Re-LEH. The new LEH enzymes have been crystallized and their structures solved to high resolution in the native form and in complex with the inhibitor valpromide for Tomsk-LEH and poly(ethylene glycol) for CH55-LEH. The structural analysis has provided insights into the LEH mechanism, substrate specificity and stereoselectivity of these new LEH enzymes, which has been supported by mutagenesis studies.
Collapse
Affiliation(s)
- Erica Elisa Ferrandi
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Milano, Italy.,University of Copenhagen, Denmark
| | - Christopher Sayer
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, UK
| | - Michail N Isupov
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, UK
| | - Celeste Annovazzi
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Milano, Italy
| | - Carlotta Marchesi
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Milano, Italy
| | - Gianluca Iacobone
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Milano, Italy
| | - Xu Peng
- University of Copenhagen, Denmark
| | | | | | - Jennifer A Littlechild
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, UK
| | - Daniela Monti
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Milano, Italy
| |
Collapse
|
27
|
Li H, Fei Z, Gong J, Yang T, Xu Z, Shi J. Screening and characterization of a highly active chitosanase based on metagenomic technology. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2014.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
28
|
Kim M, Yoon H, Kim Y, Kim Y, Kong W, Kim J. Comparative analysis of bacterial diversity and communities inhabiting the fairy ring of Tricholoma matsutake
by barcoded pyrosequencing. J Appl Microbiol 2014; 117:699-710. [DOI: 10.1111/jam.12572] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/10/2014] [Accepted: 05/25/2014] [Indexed: 01/08/2023]
Affiliation(s)
- M. Kim
- Department of Life Sciences and Biotechnology; Kyungpook National University; Daegu Korea
| | - H. Yoon
- Department of Life Sciences and Biotechnology; Kyungpook National University; Daegu Korea
| | - Y.E. Kim
- Department of Life Sciences and Biotechnology; Kyungpook National University; Daegu Korea
| | - Y.J. Kim
- Korea Environmental Industry and Technology Institute; Seoul Korea
| | - W.S. Kong
- Mushroom Research Division; National Institute of Horticultural and Herbal Science; Rural Development Administration; Suwon Korea
| | - J.G. Kim
- Department of Life Sciences and Biotechnology; Kyungpook National University; Daegu Korea
| |
Collapse
|
29
|
Tseng CH, Tang SL. Marine microbial metagenomics: from individual to the environment. Int J Mol Sci 2014; 15:8878-92. [PMID: 24857918 PMCID: PMC4057765 DOI: 10.3390/ijms15058878] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 04/29/2014] [Accepted: 05/08/2014] [Indexed: 01/12/2023] Open
Abstract
Microbes are the most abundant biological entities on earth, therefore, studying them is important for understanding their roles in global ecology. The science of metagenomics is a relatively young field of research that has enjoyed significant effort since its inception in 1998. Studies using next-generation sequencing techniques on single genomes and collections of genomes have not only led to novel insights into microbial genomics, but also revealed a close association between environmental niches and genome evolution. Herein, we review studies investigating microbial genomics (largely in the marine ecosystem) at the individual and community levels to summarize our current understanding of microbial ecology in the environment.
Collapse
Affiliation(s)
- Ching-Hung Tseng
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 11529, Taiwan.
| | - Sen-Lin Tang
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 11529, Taiwan.
| |
Collapse
|
30
|
Hansen NCK, Mydland LT, Næsset JA, Austbø D, Måge I, Rudi K. Molecular diversity of the equine caecal microbiota and its correlation to postprandial fermentation metabolites: A preliminary approach. ACTA AGR SCAND A-AN 2014. [DOI: 10.1080/09064702.2013.877520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
31
|
Stepankova V, Bidmanova S, Koudelakova T, Prokop Z, Chaloupkova R, Damborsky J. Strategies for Stabilization of Enzymes in Organic Solvents. ACS Catal 2013. [DOI: 10.1021/cs400684x] [Citation(s) in RCA: 415] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Veronika Stepankova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
- Enantis,
Ltd., Palackeho trida
1802/129, 612 00 Brno, Czech Republic
| | - Sarka Bidmanova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Tana Koudelakova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- Enantis,
Ltd., Palackeho trida
1802/129, 612 00 Brno, Czech Republic
| | - Radka Chaloupkova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
- Enantis,
Ltd., Palackeho trida
1802/129, 612 00 Brno, Czech Republic
| |
Collapse
|
32
|
Muth T, Benndorf D, Reichl U, Rapp E, Martens L. Searching for a needle in a stack of needles: challenges in metaproteomics data analysis. MOLECULAR BIOSYSTEMS 2013; 9:578-85. [PMID: 23238088 DOI: 10.1039/c2mb25415h] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In the past years the integral study of microbial communities of varying complexity has gained increasing research interest. Mass spectrometry-driven metaproteomics enables the analysis of such communities on the functional level, but this fledgling field still faces various technical and semantic challenges regarding experimental data analysis and interpretation. In the present review, we outline the hurdles involved and attempt to cover the most valuable methods and software implementations available to researchers in the field today. Beyond merely focusing on protein identification, we provide an overview on different data pre- and post-processing steps, such as metabolic pathway analysis, that can be useful in a typical metaproteomics workflow. Finally, we briefly discuss directions for future work.
Collapse
Affiliation(s)
- Thilo Muth
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | | | | | | | | |
Collapse
|
33
|
Eikmeyer FG, Köfinger P, Poschenel A, Jünemann S, Zakrzewski M, Heinl S, Mayrhuber E, Grabherr R, Pühler A, Schwab H, Schlüter A. Metagenome analyses reveal the influence of the inoculant Lactobacillus buchneri CD034 on the microbial community involved in grass ensiling. J Biotechnol 2013; 167:334-43. [PMID: 23880441 DOI: 10.1016/j.jbiotec.2013.07.021] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/10/2013] [Accepted: 07/10/2013] [Indexed: 10/26/2022]
Abstract
Silage is green fodder conserved by lactic acid fermentation performed by epiphytic lactic acid bacteria under anaerobic conditions. To improve the ensiling process and the quality of the resulting silage, starter cultures are added to the fresh forage. A detailed analysis of the microbial community playing a role in grass ensiling has been carried out by high throughput sequencing technologies. Moreover, the influence of the inoculant Lactobacillus buchneri CD034 on the microbial community composition was studied. For this purpose, grass was ensiled untreated or inoculated with L. buchneri CD034. The fresh forage as well as silages after 14 and 58 days of fermentation were characterized physico-chemically. Characteristic silage conditions such as increased titers of lactic acid bacteria and higher concentrations of acetic acid were observed in the inoculated silage in comparison to the untreated samples. Taxonomic community profiles deduced from 16S rDNA amplicon sequences indicated that the relative abundance of Lactococci diminished in the course of fermentations and that the proportion of bacteria belonging to the phyla Proteobacteria and Bacteroidetes increased during the fermentation of untreated silage. In the inoculated silage, members of these phyla were repressed due to an increased abundance of Lactobacilli. In addition, metagenome analyses of silage samples confirmed taxonomic profiles based on 16S rDNA amplicons. Moreover, Lactobacillus plantarum, Lactobacillus brevis and Lactococcus lactis were found to be dominant species within silages as analyzed by means of fragment recruitments of metagenomic sequence reads on complete reference genome sequences. Fragment recruitments also provided clear evidence for the competitiveness of the inoculant strain L. buchneri CD034 during the fermentation of the inoculated silage. The inoculation strain was able to outcompete other community members and also affected physico-chemical characteristics of the silage.
Collapse
Affiliation(s)
- Felix G Eikmeyer
- Institute for Genome Research and Systems Biology, Center for Biotechnology, Bielefeld University, D-33594 Bielefeld, Germany
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Hettich RL, Pan C, Chourey K, Giannone RJ. Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities. Anal Chem 2013; 85:4203-14. [PMID: 23469896 PMCID: PMC3696428 DOI: 10.1021/ac303053e] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The availability of extensive genome information for many different microbes, including unculturable species in mixed communities from environmental samples, has enabled systems-biology interrogation by providing a means to access genomic, transcriptomic, and proteomic information. To this end, metaproteomics exploits the power of high-performance mass spectrometry for extensive characterization of the complete suite of proteins expressed by a microbial community in an environmental sample.
Collapse
|
35
|
Recent advances in the discovery and development of marine microbial natural products. Mar Drugs 2013; 11:700-17. [PMID: 23528949 PMCID: PMC3705366 DOI: 10.3390/md11030700] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 01/25/2013] [Accepted: 02/06/2013] [Indexed: 01/05/2023] Open
Abstract
Marine microbial natural products (MMNPs) have attracted increasing attention from microbiologists, taxonomists, ecologists, agronomists, chemists and evolutionary biologists during the last few decades. Numerous studies have indicated that diverse marine microbes appear to have the capacity to produce an impressive array of MMNPs exhibiting a wide variety of biological activities such as antimicrobial, anti-tumor, anti-inflammatory and anti-cardiovascular agents. Marine microorganisms represent an underexplored reservoir for the discovery of MMNPs with unique scaffolds and for exploitation in the pharmaceutical and agricultural industries. This review focuses on MMNPs discovery and development over the past decades, including innovative isolation and culture methods, strategies for discovering novel MMNPs via routine screenings, metagenomics, genomics, combinatorial biosynthesis, and synthetic biology. The potential problems and future directions for exploring MMNPs are also discussed.
Collapse
|
36
|
Choi S, Chang MS, Stuecker T, Chung C, Newcombe DA, Venkateswaran K. A fosmid cloning strategy for detecting the widest possible spectrum of microbes from the international space station drinking water system. Genomics Inform 2013; 10:249-55. [PMID: 23346038 PMCID: PMC3543926 DOI: 10.5808/gi.2012.10.4.249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 10/28/2012] [Accepted: 11/05/2012] [Indexed: 12/04/2022] Open
Abstract
In this study, fosmid cloning strategies were used to assess the microbial populations in water from the International Space Station (ISS) drinking water system (henceforth referred to as Prebiocide and Tank A water samples). The goals of this study were: to compare the sensitivity of the fosmid cloning strategy with that of traditional culture-based and 16S rRNA-based approaches and to detect the widest possible spectrum of microbial populations during the water purification process. Initially, microbes could not be cultivated, and conventional PCR failed to amplify 16S rDNA fragments from these low biomass samples. Therefore, randomly primed rolling-circle amplification was used to amplify any DNA that might be present in the samples, followed by size selection by using pulsed-field gel electrophoresis. The amplified high-molecular-weight DNA from both samples was cloned into fosmid vectors. Several hundred clones were randomly selected for sequencing, followed by Blastn/Blastx searches. Sequences encoding specific genes from Burkholderia, a species abundant in the soil and groundwater, were found in both samples. Bradyrhizobium and Mesorhizobium, which belong to rhizobia, a large community of nitrogen fixers often found in association with plant roots, were present in the Prebiocide samples. Ralstonia, which is prevalent in soils with a high heavy metal content, was detected in the Tank A samples. The detection of many unidentified sequences suggests the presence of potentially novel microbial fingerprints. The bacterial diversity detected in this pilot study using a fosmid vector approach was higher than that detected by conventional 16S rRNA gene sequencing.
Collapse
Affiliation(s)
- Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea. ; Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
| | | | | | | | | | | |
Collapse
|
37
|
|
38
|
Kim S, Duc Ngo T, Kim KK, Kim TD. Characterization, crystallization and preliminary X-ray diffraction analysis of an (S)-specific esterase (pfEstA) from Pseudomonas fluorescens KCTC 1767: enantioselectivity for potential industrial applications. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1374-7. [PMID: 23143253 PMCID: PMC3515385 DOI: 10.1107/s1744309112040626] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 09/26/2012] [Indexed: 11/10/2022]
Abstract
The structures and reaction mechanisms of enantioselective hydrolases, which can be used in industrial applications such as biotransformations, are largely unknown. Here, the X-ray crystallographic study of a novel (S)-specific esterase (pfEstA) from Pseudomonas fluorescens KCTC 1767, which can be used in the production of (S)-ketoprofen, is described. Multiple sequence alignments with other hydrolases revealed that pfEstA contains a conserved Ser67 within the S-X-X-K motif as well as a highly conserved Tyr156. Recombinant protein containing an N-terminal His tag was expressed in Escherichia coli, purified to homogeneity and characterized using SDS-PAGE, MALDI-TOF MS and enantioselective analysis. pfEstA was crystallized using a solution consisting of 1 M sodium citrate, 0.1 M CHES pH 9.5, and X-ray diffraction data were collected to a resolution of 1.9 Å with an Rmerge of 7.9%. The crystals of pfEstA belonged to space group P2(1)2(1)2(1), with unit-cell parameters a=65.31, b=82.13, c=100.41 Å, α=β=γ=90°.
Collapse
Affiliation(s)
- Seulgi Kim
- Department of Molecular Science and Technology, Graduate School of Interdisciplinary Programs, Ajou University, Suwon 443-749, Republic of Korea
| | - Tri Duc Ngo
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - T. Doohun Kim
- Department of Molecular Science and Technology, Graduate School of Interdisciplinary Programs, Ajou University, Suwon 443-749, Republic of Korea
| |
Collapse
|
39
|
Cheema TA, Jirajaroenrat K, Sirinarumitr T, Rakshit SK. Isolation of a Gene Encoding a Cellulolytic Enzyme from Swamp Buffalo Rumen Metagenomes and Its Cloning and Expression inEscherichia Coli. Anim Biotechnol 2012; 23:261-77. [DOI: 10.1080/10495398.2012.722156] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
40
|
Artificial chromosomes to explore and to exploit biosynthetic capabilities of actinomycetes. J Biomed Biotechnol 2012; 2012:462049. [PMID: 22919271 PMCID: PMC3420335 DOI: 10.1155/2012/462049] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 06/20/2012] [Accepted: 07/04/2012] [Indexed: 12/02/2022] Open
Abstract
Actinomycetes are an important source of biologically active compounds, like antibiotics, antitumor agents, and immunosuppressors. Genome sequencing is revealing that this class of microorganisms has larger genomes relative to other bacteria and uses a considerable fraction of its coding capacity (5–10%) for the production of mostly cryptic secondary metabolites. To access actinomycetes biosynthetic capabilities or to improve the pharmacokinetic properties and production yields of these chemically complex compounds, genetic manipulation of the producer strains can be performed. Heterologous expression in amenable hosts can be useful to exploit and to explore the genetic potential of actinomycetes and not cultivable but interesting bacteria. Artificial chromosomes that can be stably integrated into the Streptomyces genome were constructed and demonstrated to be effective for transferring entire biosynthetic gene clusters from intractable actinomycetes into more suitable hosts. In this paper, the construction of several shuttle Escherichia coli-Streptomyces artificial chromosomes is discussed together with old and new strategies applied to improve heterologous production of secondary metabolites.
Collapse
|
41
|
Santamaria M, Fosso B, Consiglio A, De Caro G, Grillo G, Licciulli F, Liuni S, Marzano M, Alonso-Alemany D, Valiente G, Pesole G. Reference databases for taxonomic assignment in metagenomics. Brief Bioinform 2012; 13:682-95. [PMID: 22786784 DOI: 10.1093/bib/bbs036] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Metagenomics is providing an unprecedented access to the environmental microbial diversity. The amplicon-based metagenomics approach involves the PCR-targeted sequencing of a genetic locus fitting different features. Namely, it must be ubiquitous in the taxonomic range of interest, variable enough to discriminate between different species but flanked by highly conserved sequences, and of suitable size to be sequenced through next-generation platforms. The internal transcribed spacers 1 and 2 (ITS1 and ITS2) of the ribosomal DNA operon and one or more hyper-variable regions of 16S ribosomal RNA gene are typically used to identify fungal and bacterial species, respectively. In this context, reliable reference databases and taxonomies are crucial to assign amplicon sequence reads to the correct phylogenetic ranks. Several resources provide consistent phylogenetic classification of publicly available 16S ribosomal DNA sequences, whereas the state of ribosomal internal transcribed spacers reference databases is notably less advanced. In this review, we aim to give an overview of existing reference resources for both types of markers, highlighting strengths and possible shortcomings of their use for metagenomics purposes. Moreover, we present a new database, ITSoneDB, of well annotated and phylogenetically classified ITS1 sequences to be used as a reference collection in metagenomic studies of environmental fungal communities. ITSoneDB is available for download and browsing at http://itsonedb.ba.itb.cnr.it/.
Collapse
Affiliation(s)
- Monica Santamaria
- Institute of Biomembranes and Bioenergetics, National Research Council, Bari, Italy
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Hettich RL, Sharma R, Chourey K, Giannone RJ. Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities. Curr Opin Microbiol 2012; 15:373-80. [PMID: 22632760 DOI: 10.1016/j.mib.2012.04.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 04/27/2012] [Indexed: 10/28/2022]
Abstract
The availability of genome information for microbial consortia, including unculturable species, from environmental samples has enabled systems-biology interrogation by providing a means to access genomic, transcriptomic, and proteomic information. This provides a unique opportunity to characterize the molecular activities and interactions of these microbial systems at a comprehensive level never before possible. Such information not only provides details about the organizational, functional, and metabolic activities of such systems, but also the untapped reserve of molecular activities that might be invoked and exploited under certain environmental conditions. Since bacteria naturally exist in complex ecosystems, it is imperative to develop and utilize analytical approaches that can provide molecular level details on systems consisting of mixed microbial membership. This is the realm of metaproteomics-the characterization of the complement of proteins expressed by a microbial community in an environmental sample.
Collapse
|
43
|
Patowary A, Chauhan RK, Singh M, Kv S, Periwal V, Kp K, Sapkal GN, Bondre VP, Gore MM, Sivasubbu S, Scaria V. De novo identification of viral pathogens from cell culture hologenomes. BMC Res Notes 2012; 5:11. [PMID: 22226071 PMCID: PMC3284880 DOI: 10.1186/1756-0500-5-11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Accepted: 01/06/2012] [Indexed: 11/12/2022] Open
Abstract
Background Fast, specific identification and surveillance of pathogens is the cornerstone of any outbreak response system, especially in the case of emerging infectious diseases and viral epidemics. This process is generally tedious and time-consuming thus making it ineffective in traditional settings. The added complexity in these situations is the non-availability of pure isolates of pathogens as they are present as mixed genomes or hologenomes. Next-generation sequencing approaches offer an attractive solution in this scenario as it provides adequate depth of sequencing at fast and affordable costs, apart from making it possible to decipher complex interactions between genomes at a scale that was not possible before. The widespread application of next-generation sequencing in this field has been limited by the non-availability of an efficient computational pipeline to systematically analyze data to delineate pathogen genomes from mixed population of genomes or hologenomes. Findings We applied next-generation sequencing on a sample containing mixed population of genomes from an epidemic with appropriate processing and enrichment. The data was analyzed using an extensive computational pipeline involving mapping to reference genome sets and de-novo assembly. In depth analysis of the data generated revealed the presence of sequences corresponding to Japanese encephalitis virus. The genome of the virus was also independently de-novo assembled. The presence of the virus was in addition, verified using standard molecular biology techniques. Conclusions Our approach can accurately identify causative pathogens from cell culture hologenome samples containing mixed population of genomes and in principle can be applied to patient hologenome samples without any background information. This methodology could be widely applied to identify and isolate pathogen genomes and understand their genomic variability during outbreaks.
Collapse
Affiliation(s)
- Ashok Patowary
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Wang J, Xiong Z, Meng H, Wang Y, Wang Y. Synthetic biology triggers new era of antibiotics development. Subcell Biochem 2012; 64:95-114. [PMID: 23080247 DOI: 10.1007/978-94-007-5055-5_5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
As a discipline to design and construct organisms with desired properties, synthetic biology has generated rapid progresses in the last decade. Combined synthetic biology with the traditional process, a new universal workflow for drug development has been becoming more and more attractive. The new methodology exhibits more efficient and inexpensive comparing to traditional methods in every aspect, such as new compounds discovery & screening, process design & drug manufacturing. This article reviews the application of synthetic biology in antibiotics development, including new drug discovery and screening, combinatorial biosynthesis to generate more analogues and heterologous expression of biosynthetic gene clusters with systematic engineering the recombinant microbial systems for large scale production.
Collapse
Affiliation(s)
- Jianfeng Wang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | | | | | | | | |
Collapse
|
45
|
Lidder P, Sonnino A. Biotechnologies for the management of genetic resources for food and agriculture. ADVANCES IN GENETICS 2012; 78:1-167. [PMID: 22980921 DOI: 10.1016/b978-0-12-394394-1.00001-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In recent years, the land area under agriculture has declined as also has the rate of growth in agricultural productivity while the demand for food continues to escalate. The world population now stands at 7 billion and is expected to reach 9 billion in 2045. A broad range of agricultural genetic diversity needs to be available and utilized in order to feed this growing population. Climate change is an added threat to biodiversity that will significantly impact genetic resources for food and agriculture (GRFA) and food production. There is no simple, all-encompassing solution to the challenges of increasing productivity while conserving genetic diversity. Sustainable management of GRFA requires a multipronged approach, and as outlined in the paper, biotechnologies can provide powerful tools for the management of GRFA. These tools vary in complexity from those that are relatively simple to those that are more sophisticated. Further, advances in biotechnologies are occurring at a rapid pace and provide novel opportunities for more effective and efficient management of GRFA. Biotechnology applications must be integrated with ongoing conventional breeding and development programs in order to succeed. Additionally, the generation, adaptation, and adoption of biotechnologies require a consistent level of financial and human resources and appropriate policies need to be in place. These issues were also recognized by Member States at the FAO international technical conference on Agricultural Biotechnologies for Developing Countries (ABDC-10), which took place in March 2010 in Mexico. At the end of the conference, the Member States reached a number of key conclusions, agreeing, inter alia, that developing countries should significantly increase sustained investments in capacity building and the development and use of biotechnologies to maintain the natural resource base; that effective and enabling national biotechnology policies and science-based regulatory frameworks can facilitate the development and appropriate use of biotechnologies in developing countries; and that FAO and other relevant international organizations and donors should significantly increase their efforts to support the strengthening of national capacities in the development and appropriate use of pro-poor agricultural biotechnologies.
Collapse
Affiliation(s)
- Preetmoninder Lidder
- Office of Knowledge Exchange, Research and Extension, Research and Extension Branch, Food and Agriculture Organization of the UN (FAO), Viale delle Terme di Caracalla, Rome, Italy
| | - Andrea Sonnino
- Office of Knowledge Exchange, Research and Extension, Research and Extension Branch, Food and Agriculture Organization of the UN (FAO), Viale delle Terme di Caracalla, Rome, Italy
| |
Collapse
|
46
|
Abstract
Genome walking is a molecular procedure for the direct identification of nucleotide sequences from purified genomes. The only requirement is the availability of a known nucleotide sequence from which to start. Several genome walking methods have been developed in the last 20 years, with continuous improvements added to the first basic strategies, including the recent coupling with next generation sequencing technologies. This review focuses on the use of genome walking strategies in several aspects of the study of eukaryotic genomes. In a first part, the analysis of the numerous strategies available is reported. The technical aspects involved in genome walking are particularly intriguing, also because they represent the synthesis of the talent, the fantasy and the intelligence of several scientists. Applications in which genome walking can be employed are systematically examined in the second part of the review, showing the large potentiality of this technique, including not only the simple identification of nucleotide sequences but also the analysis of large collections of mutants obtained from the insertion of DNA of viral origin, transposons and transfer DNA (T-DNA) constructs. The enormous amount of data obtained indicates that genome walking, with its large range of applicability, multiplicity of strategies and recent developments, will continue to have much to offer for the rapid identification of unknown sequences in several fields of genomic research.
Collapse
Affiliation(s)
- Claudia Leoni
- Department of Biochemistry and Molecular Biology, University of Bari, Bari, Italy
| | | | | | | | | |
Collapse
|
47
|
DeSantis TZ, Keller K, Karaoz U, Alekseyenko AV, Singh NNS, Brodie EL, Pei Z, Andersen GL, Larsen N. Simrank: Rapid and sensitive general-purpose k-mer search tool. BMC Ecol 2011; 11:11. [PMID: 21524302 PMCID: PMC3097142 DOI: 10.1186/1472-6785-11-11] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 04/27/2011] [Indexed: 02/01/2023] Open
Abstract
Background Terabyte-scale collections of string-encoded data are expected from consortia efforts such as the Human Microbiome Project http://nihroadmap.nih.gov/hmp. Intra- and inter-project data similarity searches are enabled by rapid k-mer matching strategies. Software applications for sequence database partitioning, guide tree estimation, molecular classification and alignment acceleration have benefited from embedded k-mer searches as sub-routines. However, a rapid, general-purpose, open-source, flexible, stand-alone k-mer tool has not been available. Results Here we present a stand-alone utility, Simrank, which allows users to rapidly identify database strings the most similar to query strings. Performance testing of Simrank and related tools against DNA, RNA, protein and human-languages found Simrank 10X to 928X faster depending on the dataset. Conclusions Simrank provides molecular ecologists with a high-throughput, open source choice for comparing large sequence sets to find similarity.
Collapse
Affiliation(s)
- Todd Z DeSantis
- Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Jiang C, Li SX, Luo FF, Jin K, Wang Q, Hao ZY, Wu LL, Zhao GC, Ma GF, Shen PH, Tang XL, Wu B. Biochemical characterization of two novel β-glucosidase genes by metagenome expression cloning. BIORESOURCE TECHNOLOGY 2011; 102:3272-3278. [PMID: 20971635 DOI: 10.1016/j.biortech.2010.09.114] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 09/28/2010] [Accepted: 09/28/2010] [Indexed: 05/30/2023]
Abstract
Two novel β-glucosidase genes designated as bgl1D and bgl1E, which encode 172- and 151-aa peptides, respectively, were cloned by function-based screening of a metagenomic library from uncultured soil microorganisms. Sequence analyses indicated that Bgl1D and Bgl1E exhibited lower similarities with some putative β-glucosidases. Functional characterization through high-performance liquid chromatography demonstrated that purified recombinant Bgl1D and Bgl1E proteins hydrolyzed D-glucosyl-β-(1-4)-D-glucose to glucose. Using p-nitrophenyl-β-D-glucoside as substrate, K(m) was 0.54 and 2.11 mM, and k(cat)/K(m) was 1489 and 787 mM(-1) min(-1) for Bgl1D and Bgl1E, respectively. The optimum pH and temperature for Bgl1D was pH 10.0 and 30°C, while the optimum values for Bgl1E were pH 10.0 and 25°C. Bgl1D exhibited habitat-specific characteristics, including higher activity in lower temperature and at high concentrations of AlCl(3) and LiCl. Bgl1D also displayed remarkable activity across a broad pH range (5.5-10.5), making it a potential candidate for industrial applications.
Collapse
Affiliation(s)
- Chengjian Jiang
- Guangxi Key Laboratory of Subtropical Bioresources Conservation and Utilization, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, People's Republic of China
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Hanning IB, Ricke SC. Prescreening of microbial populations for the assessment of sequencing potential. Methods Mol Biol 2011; 733:159-170. [PMID: 21431769 DOI: 10.1007/978-1-61779-089-8_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Next-generation sequencing (NGS) is a powerful tool that can be utilized to profile and compare microbial populations. By amplifying a target gene present in all bacteria and subsequently sequencing amplicons, the bacteria genera present in the populations can be identified and compared. In some scenarios, little to no difference may exist among microbial populations being compared in which case a prescreening method would be practical to determine which microbial populations would be suitable for further analysis by NGS. Denaturing density-gradient electrophoresis (DGGE) is relatively cheaper than NGS and the data comparing microbial populations are ready to be viewed immediately after electrophoresis. DGGE follows essentially the same initial methodology as NGS by targeting and amplifying the 16S rRNA gene. However, as opposed to sequencing amplicons, DGGE amplicons are analyzed by electrophoresis. By prescreening microbial populations with DGGE, more efficient use of NGS methods can be accomplished. In this chapter, we outline the protocol for DGGE targeting the same gene (16S rRNA) that would be targeted for NGS to compare and determine differences in microbial populations from a wide range of ecosystems.
Collapse
Affiliation(s)
- Irene B Hanning
- Department of Food Science and Technology, University of Tennessee, Knoxville, TN, USA.
| | | |
Collapse
|
50
|
Abstract
Metagenomics literally means "beyond the genome." Marine microbial metagenomic databases presently comprise approximately 400 billion base pairs of DNA, only approximately 3% of that found in 1 ml of seawater. Very soon a trillion-base-pair sequence run will be feasible, so it is time to reflect on what we have learned from metagenomics. We review the impact of metagenomics on our understanding of marine microbial communities. We consider the studies facilitated by data generated through the Global Ocean Sampling expedition, as well as the revolution wrought at the individual laboratory level through next generation sequencing technologies. We review recent studies and discoveries since 2008, provide a discussion of bioinformatic analyses, including conceptual pipelines and sequence annotation and predict the future of metagenomics, with suggestions of collaborative community studies tailored toward answering some of the fundamental questions in marine microbial ecology.
Collapse
Affiliation(s)
- Jack A Gilbert
- Plymouth Marine Laboratory, Plymouth PL1 3DH, United Kingdom.
| | | |
Collapse
|