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Kendlbacher V, Winter TMR, Bright M. Zoothamnium mariella sp. nov., a marine, colonial ciliate with an atypcial growth pattern, and its ectosymbiont Candidatus Fusimicrobium zoothamnicola gen. nov., sp. nov. PLoS One 2024; 19:e0300758. [PMID: 38557976 PMCID: PMC10984469 DOI: 10.1371/journal.pone.0300758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
Ciliates are unicellular eukaryotes, regularly involved in symbiotic associations. Symbionts may colonize the inside of their cells as well as their surface as ectosymbionts. Here, we report on a new ciliate species, designated as Zoothamnium mariella sp. nov. (Peritrichia, Sessilida), discovered in the northern Adriatic Sea (Mediterranean Sea) in 2021. We found this ciliate species to be monospecifically associated with a new genus of ectosymbiotic bacteria, here proposed as Candidatus Fusimicrobium zoothamnicola gen. nov., sp. nov. To formally describe the new ciliate species, we investigated its morphology and sequenced its 18S rRNA gene. To demonstrate its association with a single species of bacterial ectosymbiont, we performed 16S rRNA gene sequencing, fluorescence in situ hybridization, and scanning electron microscopy. Additionally, we explored the two partners' cultivation requirements and ecology. Z. mariella sp. nov. was characterized by a colony length of up to 1 mm. A consistent number of either seven or eight long branches alternated on the stalk in close distance to each other. The colony developed three different types of zooids: microzooids ("trophic stage"), macrozooids ("telotroch stage"), and terminal zooids ("dividing stage"). Viewed from inside the cell, the microzooids' oral ciliature ran in 1 ¼ turns in a clockwise direction around the peristomial disc before entering the infundibulum, where it performed another ¾ turn. Phylogenetic analyses assigned Z. mariella sp. nov. to clade II of the family Zoothamnidae. The ectosymbiont formed a monophyletic clade within the Gammaproteobacteria along with two other ectosymbionts of peritrichous ciliates and a free-living vent bacterium. It colonized the entire surface of its ciliate host, except for the most basal stalk of large colonies, and exhibited a single, spindle-shaped morphotype. Furthermore, the two partners together appear to be generalists of temperate, oxic, marine shallow-water environments and were collectively cultivable in steady flow-through systems.
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Affiliation(s)
- Vincent Kendlbacher
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | | | - Monika Bright
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
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2
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Shamshitov A, Kadžienė G, Supronienė S. The Role of Soil Microbial Consortia in Sustainable Cereal Crop Residue Management. PLANTS (BASEL, SWITZERLAND) 2024; 13:766. [PMID: 38592825 PMCID: PMC10974107 DOI: 10.3390/plants13060766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 04/11/2024]
Abstract
The global escalation in cereal production, essential to meet growing population demands, simultaneously augments the generation of cereal crop residues, estimated annually at approximately 3107 × 106 Mg/year. Among different crop residue management approaches, returning them to the soil can be essential for various ecological benefits, including nutrient recycling and soil carbon sequestration. However, the recalcitrant characteristics of cereal crop residues pose significant challenges in their management, particularly in the decomposition rate. Therefore, in this review, we aim to summarize the influence of different agricultural practices on enhancing soil microbial decomposer communities, thereby effectively managing cereal crop residues. Moreover, this manuscript provides indirect estimates of cereal crop residue production in Northern Europe and Lithuania, and highlights the diverse roles of lignocellulolytic microorganisms in the decomposition process, with a particular focus on enzymatic activities. This review bridges the knowledge gap and indicates future research directions concerning the influence of agricultural practices on cereal crop residue-associated microbial consortia.
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Affiliation(s)
- Arman Shamshitov
- Laboratory of Microbiology, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Instituto al. 1, Akademija, LT-58344 Kedainiai, Lithuania;
| | - Gražina Kadžienė
- Department of Soil and Crop Management, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Instituto al. 1, Akademija, LT-58344 Kedainiai, Lithuania
| | - Skaidrė Supronienė
- Laboratory of Microbiology, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Instituto al. 1, Akademija, LT-58344 Kedainiai, Lithuania;
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Li Y, Shi X, Tan W, Ling Q, Pei F, Luo S, Qin P, Yuan H, Huang L, Yu F. Metagenomics combined with metabolomics reveals the effect of Enterobacter sp. inoculation on the rhizosphere microenvironment of Bidens pilosa L. in heavy metal contaminated soil. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:132033. [PMID: 37453352 DOI: 10.1016/j.jhazmat.2023.132033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/24/2023] [Accepted: 07/09/2023] [Indexed: 07/18/2023]
Abstract
Metagenomics analysis was performed to determine the effects of Enterobacter sp. FM-1 (FM-1) on key genera as well as functional genes in the rhizosphere of Bidens pilosa L. (B. pilosa L.). Moreover, metabolomics was used to reveal the differences among rhizosphere metabolites after FM-1 inoculation. FM-1 inoculation significantly increased the activity of enzymes associated with the carbon cycle in soil; among them, invertase activity increased by 5.52 units compared to a control. Specifically, the relative abundance of beneficial genera increased significantly, such as Lysobacter (0.45-2.58 unit increase) in low-contamination soils (LC) and Pseudomonas (31.17-45.99 unit increase) in high-contamination soils (HC). Comparison of different transformation processes of the C cycle revealed that inoculation of FM-1 increased the abundance of functional genes related to the carbon cycle in LC soil. In contrast, the nitrogen cycling pathway was significantly elevated in both the LC and HC soils. FM-1 inoculation reduced HM resistance gene abundance in the rhizosphere soil of B. pilosa L. in the LC soil. Moreover, FM-1 and B. pilosa L. interactions promoted the secretion of rhizosphere metabolites, in which lipids and amino acids played important roles in the phytoremediation process. Overall, we explored the rhizosphere effects induced by plantmicrobe interactions, providing new insights into the functional microbes and rhizosphere metabolites involved in phytoremediation.
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Affiliation(s)
- Yi Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China; College of Environment and Resources, Guangxi Normal University, Guilin, China; Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, China
| | - Xinwei Shi
- College of Environment and Resources, Guangxi Normal University, Guilin, China
| | - Weilan Tan
- College of Environment and Resources, Guangxi Normal University, Guilin, China
| | - Qiujie Ling
- College of Environment and Resources, Guangxi Normal University, Guilin, China
| | - Fengmei Pei
- College of Environment and Resources, Guangxi Normal University, Guilin, China
| | - Shiyu Luo
- College of Environment and Resources, Guangxi Normal University, Guilin, China
| | - Peiqing Qin
- College of Environment and Resources, Guangxi Normal University, Guilin, China
| | - Huijian Yuan
- Hunan Suining Huayuange National Wetland Park, Suining, China
| | - Liuan Huang
- Hunan Suining Huayuange National Wetland Park, Suining, China
| | - Fangming Yu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China; College of Environment and Resources, Guangxi Normal University, Guilin, China; Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, China.
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Developing a Temperature-Inducible Transcriptional Rheostat in Neurospora crassa. mBio 2023; 14:e0329122. [PMID: 36744948 PMCID: PMC9973361 DOI: 10.1128/mbio.03291-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Heat shock protein (HSP)-encoding genes (hsp), part of the highly conserved heat shock response (HSR), are known to be induced by thermal stress in several organisms. In Neurospora crassa, three hsp genes, hsp30, hsp70, and hsp80, have been characterized; however, the role of defined cis elements in their responses to discrete changes in temperature remains largely unexplored. To fill this gap, while also aiming to obtain a reliable fungal heat shock-inducible system, we analyzed different sections of each hsp promoter by assessing the expression of real-time transcriptional reporters. Whereas all three promoters and their resected versions were acutely induced by high temperatures, only hsp30 displayed a broad range of expression and high tunability, amply exceeding other inducible promoter systems existing in Neurospora, such as quinic acid- or light-inducible ones. As proof of concept, we employed one of these promoters to control the expression of clr-2, which encodes the master regulator of Neurospora cellulolytic capabilities. The resulting strain fails to grow on cellulose at 25°C, whereas it grows robustly if heat shock pulses are delivered daily. Additionally, we designed two hsp30 synthetic promoters and characterized them, as well as the native promoters, using a gradient of high temperatures, yielding a wide range of responses to thermal stimuli. Thus, Neurospora hsp30-based promoters represent a new set of modular elements that can be used as transcriptional rheostats to adjust the expression of a gene of interest or for the implementation of regulated circuitries for synthetic biology and biotechnological strategies. IMPORTANCE A timely and dynamic response to strong temperature fluctuations is paramount for organismal biology. At the same time, inducible promoters are a powerful tool for fungal biotechnological and synthetic biology endeavors. In this work, we analyzed the activity of several N. crassa heat shock protein (hsp) promoters at a wide range of temperatures, observing that hsp30 exhibits remarkable sensitivity and a dynamic range of expression as we charted the response of this promoter to subtle increases in temperature, and also as we built and analyzed synthetic promoters based on hsp30 cis elements. As proof of concept, we tested the ability of hsp30 to provide tight control of a central process, cellulose degradation. While this study provides an unprecedented description of the regulation of the N. crassa hsp genes, it also contributes a noteworthy addition to the molecular toolset of transcriptional controllers in filamentous fungi.
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Rembelski M, Fraterrigo J. Drought reduces invasive grass performance by disrupting plant-microbe interactions that enhance plant nitrogen supply. Oecologia 2023; 201:549-564. [PMID: 36598562 DOI: 10.1007/s00442-022-05307-4] [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: 03/08/2022] [Accepted: 12/16/2022] [Indexed: 01/05/2023]
Abstract
Non-native invasive plants can promote their dominance in novel ecosystems by accelerating soil nutrient cycling via interactions with decomposer microbes. Changes in abiotic conditions associated with frequent or prolonged drought may disrupt these interactions, but the effects of disruption on invasive plant performance and the underpinning mechanisms are poorly understood. Here, we used rainout shelters in an experimental field setting to test the hypothesis that drought reduces invasive plant performance by reducing microbial metabolic activity, resulting in decreased nitrogen flow to plants. We imposed growing season drought on populations of the exotic grass Microstegium vimineum, a widespread invasive plant in eastern deciduous forests, and quantified effects on aboveground and belowground biomass, and carbon (C) and nitrogen (N) cycling among plants, decomposers, and soil. Drought resulted in a 24% decrease in soil respiration, a 16% decrease in phenol oxidase enzyme activity, a 12% decrease in dissolved organic N concentration, and a decrease in the C:N ratio of particulate organic matter, suggesting reduced microbial metabolic activity and nutrient mining of soil organic matter. Drought also reduced aboveground Microstegium biomass 33% and increased Microstegium leaf C:N ratio, consistent with a decline in plant N uptake. We conclude that drought can reduce the performance of existing invasive species populations by suppressing plant-microbe interactions that increase nitrogen supply to plants, which may have consequences for the persistence of invasive plants under hydrologic change.
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Affiliation(s)
- Mara Rembelski
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Jennifer Fraterrigo
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL, 61801, USA. .,Program in Ecology, Evolution and Conservation Biology, University of Illinois, Urbana, IL, 61801, USA.
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Kovács E, Szűcs C, Farkas A, Szuhaj M, Maróti G, Bagi Z, Rákhely G, Kovács KL. Pretreatment of lignocellulosic biogas substrates by filamentous fungi. J Biotechnol 2022; 360:160-170. [PMID: 36273669 DOI: 10.1016/j.jbiotec.2022.10.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 09/12/2022] [Accepted: 10/16/2022] [Indexed: 11/19/2022]
Abstract
Decomposition of lignocellulosic plant biomass by four filamentous fungi was carried out to facilitate subsequent anaerobic degradation and biogas formation. Agricultural side products, wheat straw and corn stover and forestry energy plant willow chips were selected as plant biomass sources. The substrates were confronted by pure cultures of Penicillium aurantiogriseum (new isolate from rumen), Trichoderma reesei (DSM768), Gilbertella persicaria (SZMC11086) and Rhizomucor miehei (SZMC11005). In addition to total cellulolytic filter paper degradation activity, the production of endoglucanase, cellobiohydrolase, β-glucosidase enzymes were followed during the pretreatment period, which lasted for 10 days at 37 °C. The products of pretreatments were subsequently tested for mesophilic biogas production in batch reactors. All 4 strains effectively pretreated the lignocellulosic substrates albeit in varying degrees, which was related to the level of the tested hydrolytic enzyme activities. Penicillium aurantiogriseum showed outstanding hydrolytic enzyme production and highest biogas yield from the partially degraded substrates. Corn stover was the best substrate for biomass decomposition and biogas production. Scanning electron microscopy confirmed the deep penetration of fungal hyphae into the lignocellulosic substrate in all cases.
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Affiliation(s)
- Etelka Kovács
- Department of Biotechnology, University of Szeged, Szeged, Hungary; Institute of Plant Biology, Biological Research Center, Szeged, Hungary
| | - Csilla Szűcs
- Department of Biotechnology, University of Szeged, Szeged, Hungary; Institute of Plant Biology, Biological Research Center, Szeged, Hungary
| | - Attila Farkas
- Institute of Plant Biology, Biological Research Center, Szeged, Hungary
| | - Márk Szuhaj
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center, Szeged, Hungary
| | - Zoltán Bagi
- Department of Biotechnology, University of Szeged, Szeged, Hungary; Institute of Plant Biology, Biological Research Center, Szeged, Hungary; Institute of Biophysics, Biological Research Center, Szeged, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary; Institute of Biophysics, Biological Research Center, Szeged, Hungary
| | - Kornél L Kovács
- Department of Biotechnology, University of Szeged, Szeged, Hungary; Institute of Plant Biology, Biological Research Center, Szeged, Hungary; Institute of Biophysics, Biological Research Center, Szeged, Hungary; Department of Oral Biology and Experimental Dentistry, University of Szeged, Szeged, Hungary.
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7
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Dederko-Kantowicz P, Sommer A, Staroszczyk H. Structural changes of bacterial cellulose due to incubation in conditions simulating human plasma in the presence of selected pathogens. Carbohydr Polym 2021; 266:118153. [PMID: 34044958 DOI: 10.1016/j.carbpol.2021.118153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/25/2021] [Accepted: 04/30/2021] [Indexed: 11/29/2022]
Abstract
Bacterial nanocellulose (BNC) is a natural biomaterial with a wide range of medical applications. However, it cannot be used as a biological implant of the circulatory system without checking whether it is biodegradable under human plasma conditions. This work aimed to investigate the BNC biodegradation by selected pathogens under conditions simulating human plasma. The BNC was incubated in simulated biological fluids with or without Staphylococcus aureus, Candida albicans and Aspergillus fumigatus, and its physicochemical properties were studied. The results showed that the incubation of BNC in simulated body fluid with A. fumigatus contributes more to its degradation than that under other conditions tested. The rearrangement of the hydrogen-bond network in this case resulted in a more compact structure, with an increased crystallinity index, reduced thermal stability and looser cross-linking. Therefore, although BNC shows great potential as a cardiovascular implant material, before use for this purpose its biodegradability should be limited.
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Affiliation(s)
- Paulina Dederko-Kantowicz
- Department of Chemistry, Technology and Biotechnology of Food, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12 St. 80-233 Gdańsk, Poland; Laboratory of Molecular Diagnostics and Biochemistry, Plant Breeding and Acclimatization Institute - National Research Institute, Bonin Research Center, Bonin 3, 76-009 Bonin, Poland.
| | - Agata Sommer
- Department of Chemistry, Technology and Biotechnology of Food, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12 St. 80-233 Gdańsk, Poland.
| | - Hanna Staroszczyk
- Department of Chemistry, Technology and Biotechnology of Food, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12 St. 80-233 Gdańsk, Poland.
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Siwach A, Kaushal S, Baishya R. Terricolous mosses impact soil microbial biomass carbon and enzymatic activity under temperate forest types of the Garhwal Himalayas. ENVIRONMENTAL MONITORING AND ASSESSMENT 2021; 193:516. [PMID: 34308502 DOI: 10.1007/s10661-021-09295-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
Estimates of enzymatic activity are used as indices for soil quality, microbial nutrient demand, microbial growth, and activity. Mosses trap soil moisture, influence soil temperature, and create a microenvironment promoting an overall higher level of microbial activity, thus making the decomposition of organic matter more favorable. This study determines the role of mosses in influencing soil biochemical properties in three temperate forest types of the Garhwal Himalayas, Uttarakhand, viz., moist temperate deciduous forest, Ban oak forest, and moist deodar forest. Activities of major soil enzymes (dehydrogenase, β-glucosidase, acid phosphatase, aryl sulfatase, phenol oxidase, and urease) and soil microbial biomass carbon (SMBC) were determined under two different substrates, i.e., with and without moss cover in two different seasons, viz., monsoon and winter. The Pearson correlation of enzymes with specific soil nutrients they act upon has also been shown. The SMBC and on average activities of all the enzymes were predominantly higher in soil with moss cover during monsoon season and without moss cover in the winter season. SMBC in the three study sites ranged from 280.55 to 1707.64 µg C/g. Statistically significant differences (p < 0.01) were observed for all the properties within the substrates among all the three sites and across the two seasons. Our results suggest that mosses play a significant role in positively influencing soil biochemical properties in both seasons by creating a microscale mosaic that offers a high degree of heterogeneity in soil function. Our study emphasizes that mosses strongly affect soil enzyme activities and microbial biomass, thus improving soil health.
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Affiliation(s)
- Anshu Siwach
- Ecology and Ecosystem Research Laboratory, Department of Botany, University of Delhi, Delhi, 110007, India
| | - Siddhartha Kaushal
- Ecology and Ecosystem Research Laboratory, Department of Botany, University of Delhi, Delhi, 110007, India
| | - Ratul Baishya
- Ecology and Ecosystem Research Laboratory, Department of Botany, University of Delhi, Delhi, 110007, India.
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Decay Process Characteristics and Fungal Community Composition of Salix psammophila Sand Barriers in an Arid Area, Northern China. SUSTAINABILITY 2021. [DOI: 10.3390/su13147590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
With the increase in setting years in deserts, Salix psammophila sand barriers with different degrees of lodging damage caused by decay are losing wind-prevention and sand-fixation properties. In this study, we focus on the change in chemical properties of soils, and physical and mechanical properties of plants along different setting years; meanwhile, the change in fungal communities has been analyzed using high-throughput sequencing technology. The results show that a change in physical and mechanical properties and the loss of primary chemical components led to the degradation of the protective properties of the barrier to different degrees. After five years of setting, the physical parameters of basic density and shrinkage rate decreased by 44.04% and 28.68%, respectively, and the loss of the modulus of rupture mechanical index declined by 62.72%. After seven years of setting, the mechanical indexes of the modulus of rupture decreased by 76.95%. Five and seven years represented important inflection points in the decay process. Sordariomycetes (53.75%) and Eurotiomycetes (19.78%) were the main fungal groups present during the decay of the sand barrier. The basic density, moisture content, cellulose, and lignin of the sand barrier were the main driving factors affecting the distribution of fungal communities. The mechanism on fungal community to the decay of sand barriers still needs further studies to keep the function of sand barriers in fragile desert ecosystems.
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Chukwuma OB, Rafatullah M, Tajarudin HA, Ismail N. A Review on Bacterial Contribution to Lignocellulose Breakdown into Useful Bio-Products. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:6001. [PMID: 34204975 PMCID: PMC8199887 DOI: 10.3390/ijerph18116001] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 12/15/2022]
Abstract
Discovering novel bacterial strains might be the link to unlocking the value in lignocellulosic bio-refinery as we strive to find alternative and cleaner sources of energy. Bacteria display promise in lignocellulolytic breakdown because of their innate ability to adapt and grow under both optimum and extreme conditions. This versatility of bacterial strains is being harnessed, with qualities like adapting to various temperature, aero tolerance, and nutrient availability driving the use of bacteria in bio-refinery studies. Their flexible nature holds exciting promise in biotechnology, but despite recent pointers to a greener edge in the pretreatment of lignocellulose biomass and lignocellulose-driven bioconversion to value-added products, the cost of adoption and subsequent scaling up industrially still pose challenges to their adoption. However, recent studies have seen the use of co-culture, co-digestion, and bioengineering to overcome identified setbacks to using bacterial strains to breakdown lignocellulose into its major polymers and then to useful products ranging from ethanol, enzymes, biodiesel, bioflocculants, and many others. In this review, research on bacteria involved in lignocellulose breakdown is reviewed and summarized to provide background for further research. Future perspectives are explored as bacteria have a role to play in the adoption of greener energy alternatives using lignocellulosic biomass.
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Affiliation(s)
| | - Mohd Rafatullah
- Division of Environmental Technology, School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (O.B.C.); (H.A.T.); (N.I.)
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Xu CY, Du C, Jian JS, Hou L, Wang ZK, Wang Q, Geng ZC. The interplay of labile organic carbon, enzyme activities and microbial communities of two forest soils across seasons. Sci Rep 2021; 11:5002. [PMID: 33654125 PMCID: PMC7925553 DOI: 10.1038/s41598-021-84217-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 02/10/2021] [Indexed: 12/26/2022] Open
Abstract
Soil labile organic carbon (LOC) responds rapidly to environmental changes and plays an important role in carbon cycle. In this study, the seasonal fluctuations in LOC, the activities of carbon-cycle related enzymes, and the bacterial and fungal communities were analyzed for soils collected from two forests, namely Betula albosinensis (Ba) and Picea asperata Mast. (Pa), in the Qinling Mountains of China. Results revealed that the seasonal average contents of microbial biomass carbon (MBC), easily oxidized organic carbon (EOC), and dissolved organic carbon (DOC) of Pa forest soil were 13.5%, 30.0% and 15.7% less than those in Ba soil. The seasonal average enzyme activities of β-1,4-glucosidase (βG), and β-1,4-xylosidase (βX) of Ba forest soils were 30.0% and 32.3% higher than those of Pa soil while the enzyme activity of cellobiohydrolase (CBH) was 19.7% lower. Furthermore, the relative abundance of Acidobacteria was significantly higher in summer than in winter, whereas the relative abundance of Bacteroidetes was higher in winter. Regarding the fungal communities, the relative abundance of Basidiomycota was lowest in winter, whereas Ascomycota predominated in the same season. In addition, the soil LOC was significantly positively correlated with the CBH, βG and βX activities. Changes in LOC were significantly correlated with Acidobacteria, Bacteroidetes and Basidiomycota. We conclude that the seasonal fluctuations in forest soil LOC fractions relied on carbon cycle-associated enzymatic activities and microorganisms, which in turn were affected by climatic conditions.
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Affiliation(s)
- Chen-Yang Xu
- College of Natural Resources and Environment, Northwest A&F University, No. 3 Taicheng Road, Yangling, 712100, Shaanxi, China.,Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Can Du
- College of Natural Resources and Environment, Northwest A&F University, No. 3 Taicheng Road, Yangling, 712100, Shaanxi, China.,Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jin-Shi Jian
- Pacific Northwest National Laboratory-University of Maryland Joint Global Change Research Institute, 5825 University Research Court, Suite 3500, College Park, MD, USA
| | - Lin Hou
- College of Forestry, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhi-Kang Wang
- College of Natural Resources and Environment, Northwest A&F University, No. 3 Taicheng Road, Yangling, 712100, Shaanxi, China.,Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qiang Wang
- College of Natural Resources and Environment, Northwest A&F University, No. 3 Taicheng Road, Yangling, 712100, Shaanxi, China.,Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zeng-Chao Geng
- College of Natural Resources and Environment, Northwest A&F University, No. 3 Taicheng Road, Yangling, 712100, Shaanxi, China. .,Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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12
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Fraterrigo JM, Rembelski MK. Frequent Fire Reduces the Magnitude of Positive Interactions Between an Invasive Grass and Soil Microbes in Temperate Forests. Ecosystems 2021. [DOI: 10.1007/s10021-021-00615-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Plant invasion impacts on fungal community structure and function depend on soil warming and nitrogen enrichment. Oecologia 2020; 194:659-672. [PMID: 33141324 PMCID: PMC7683454 DOI: 10.1007/s00442-020-04797-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/24/2020] [Indexed: 01/04/2023]
Abstract
The impacts of invasive species on biodiversity may be mitigated or exacerbated by abiotic environmental changes. Invasive plants can restructure soil fungal communities with important implications for native biodiversity and nutrient cycling, yet fungal responses to invasion may depend on numerous anthropogenic stressors. In this study, we experimentally invaded a long-term soil warming and simulated nitrogen deposition experiment with the widespread invasive plant Alliaria petiolata (garlic mustard) and tested the responses of soil fungal communities to invasion, abiotic factors, and their interaction. We focused on the phytotoxic garlic mustard because it suppresses native mycorrhizae across forests of North America. We found that invasion in combination with warming, but not under ambient conditions or elevated nitrogen, significantly reduced soil fungal biomass and ectomycorrhizal relative abundances and increased relative abundances of general soil saprotrophs and fungal genes encoding for hydrolytic enzymes. These results suggest that warming potentially exacerbates fungal responses to plant invasion. Soils collected from uninvaded and invaded plots across eight forests spanning a 4 °C temperature gradient further demonstrated that the magnitude of fungal responses to invasion was positively correlated with mean annual temperature. Our study is one of the first empirical tests to show that the impacts of invasion on fungal communities depends on additional anthropogenic pressures and were greater in concert with warming than under elevated nitrogen or ambient conditions.
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Kuramae EE, Leite MFA, Suleiman AKA, Gough CM, Castillo BT, Faller L, Franklin RB, Syring J. Wood Decay Characteristics and Interspecific Interactions Control Bacterial Community Succession in Populus grandidentata (Bigtooth Aspen). Front Microbiol 2019; 10:979. [PMID: 31143163 PMCID: PMC6520631 DOI: 10.3389/fmicb.2019.00979] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/18/2019] [Indexed: 02/01/2023] Open
Abstract
Few studies have investigated bacterial community succession and the role of bacterial decomposition over a continuum of wood decay. Here, we identified how (i) the diversity and abundance of bacteria changed along a chronosequence of decay in Populus grandidentata (bigtooth aspen); (ii) bacterial community succession was dependent on the physical and chemical characteristics of the wood; (iii) interspecific bacterial interactions may mediate community structure. Four hundred and fifty-nine taxa were identified through Illumina sequencing of 16S rRNA amplicons from samples taken along a continuum of decay, representing standing dead trees, downed wood, and soil. Community diversity increased as decomposition progressed, peaking in the most decomposed trees. While a small proportion of taxa displayed a significant pattern in regards to decay status of the host log, many bacterial taxa followed a stochastic distribution. Changes in the water availability and chemical composition of standing dead and downed trees and soil were strongly coupled with shifts in bacterial communities. Nitrogen was a major driver of succession and nitrogen-fixing taxa of the order Rhizobiales were abundant early in decomposition. Recently downed logs shared 65% of their bacterial abundance with the microbiomes of standing dead trees while only sharing 16% with soil. As decay proceeds, bacterial communities appear to respond less to shifting resource availability and more to interspecific bacterial interactions – we report an increase in both the proportion (+9.3%) and the intensity (+62.3%) of interspecific interactions in later stages of decomposition, suggesting the emergence of a more complex community structure as wood decay progresses.
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Affiliation(s)
- Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Marcio F A Leite
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Afnan K A Suleiman
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Christopher M Gough
- Department of Biology, Virginia Commonwealth University, Richmond, VA, United States
| | - Buck T Castillo
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States
| | - Lewis Faller
- Department of Biology, Linfield College, McMinnville, OR, United States
| | - Rima B Franklin
- Department of Biology, Virginia Commonwealth University, Richmond, VA, United States
| | - John Syring
- Department of Biology, Linfield College, McMinnville, OR, United States
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15
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Venable ME, Podbielski MR. Impact of substrate material on algal biofilm biomass growth. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:7256-7262. [PMID: 30648237 DOI: 10.1007/s11356-019-04148-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 01/02/2019] [Indexed: 06/09/2023]
Abstract
Algae are being grown for wastewater purification and biofuels production. Their growth on a substrate facilitates these uses by allowing facile separation of algae from the water. Here, we compare different materials to determine which would best serve this purpose. A mixed culture of Anabaena and Chlorella was grown on various synthetic and natural fiber fabric substrates in a trough system with recirculating simulated wastewater. Filter materials studied as substrates for algal growth were muslin, olefin, pellon (acrylic), two types of polyester, and two types of nylon. Biomass accumulation on the various filter substrates was recorded at 7, 14, and 28 days. Filters were weighed before and after the growth periods and changes in dry biomass were recorded. Biomass accumulation was significantly affected by the fabric type. Olefin fostered the greatest increase in biomass while nylon and polyester also supported competitive increases in biomass. Pellon showed the smallest biomass increase and muslin decreased in mass due to material disintegration. Other concerns such as abrasion resistance and UV susceptibility are discussed.
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Affiliation(s)
- Mark E Venable
- Biology Department, Appalachian State University, 572 Rivers Street, Rankin Science Building, Boone, NC, 28608, USA.
| | - Melanie R Podbielski
- Biology Department, Appalachian State University, 572 Rivers Street, Rankin Science Building, Boone, NC, 28608, USA
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16
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Tiwari S, Verma T. Cellulose as a Potential Feedstock for Cellulose Enzyme Production. Fungal Biol 2019. [DOI: 10.1007/978-3-030-14726-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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17
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Affiliation(s)
- James J. Worrall
- College of Environmental Science and Forestry, State University of New York, Syracuse, New York 13210
| | - Susan E. Anagnost
- College of Environmental Science and Forestry, State University of New York, Syracuse, New York 13210
| | - Robert A. Zabel
- College of Environmental Science and Forestry, State University of New York, Syracuse, New York 13210
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18
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Phylogenetic conservatism of thermal traits explains dispersal limitation and genomic differentiation of Streptomyces sister-taxa. ISME JOURNAL 2018; 12:2176-2186. [PMID: 29880909 DOI: 10.1038/s41396-018-0180-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 03/22/2018] [Accepted: 03/26/2018] [Indexed: 12/28/2022]
Abstract
The latitudinal diversity gradient is a pattern of biogeography observed broadly in plants and animals but largely undocumented in terrestrial microbial systems. Although patterns of microbial biogeography across broad taxonomic scales have been described in a range of contexts, the mechanisms that generate biogeographic patterns between closely related taxa remain incompletely characterized. Adaptive processes are a major driver of microbial biogeography, but there is less understanding of how microbial biogeography and diversification are shaped by dispersal limitation and drift. We recently described a latitudinal diversity gradient of species richness and intraspecific genetic diversity in Streptomyces by using a geographically explicit culture collection. Within this geographically explicit culture collection, we have identified Streptomyces sister-taxa whose geographic distribution is delimited by latitude. These sister-taxa differ in geographic distribution, genomic diversity, and ecological traits despite having nearly identical SSU rRNA gene sequences. Comparative genomic analysis reveals genomic differentiation of these sister-taxa consistent with restricted gene flow across latitude. Furthermore, we show phylogenetic conservatism of thermal traits between the sister-taxa suggesting that thermal trait adaptation limits dispersal and gene flow across climate regimes as defined by latitude. Such phylogenetic conservatism of thermal traits is commonly associated with latitudinal diversity gradients for plants and animals. These data provide further support for the hypothesis that the Streptomyces latitudinal diversity gradient was formed as a result of historical demographic processes defined by dispersal limitation and driven by paleoclimate dynamics.
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19
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Nutrient Dynamics in Decomposing Dead Wood in the Context of Wood Eater Requirements: The Ecological Stoichiometry of Saproxylophagous Insects. SAPROXYLIC INSECTS 2018. [DOI: 10.1007/978-3-319-75937-1_13] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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20
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Bacteria alone establish the chemical basis of the wood-fall chemosynthetic ecosystem in the deep-sea. ISME JOURNAL 2017; 12:367-379. [PMID: 28984846 PMCID: PMC5776450 DOI: 10.1038/ismej.2017.163] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 06/29/2017] [Accepted: 08/24/2017] [Indexed: 01/05/2023]
Abstract
Wood-fall ecosystems host chemosynthetic bacteria that use hydrogen sulfide as an electron donor. The production of hydrogen sulfide from decaying wood in the deep-sea has long been suspected to rely on the activity of wood-boring bivalves, Xylophaga spp. However, recent mesocosm experiments have shown hydrogen sulfide production in the absence of wood borers. Here, we combined in situ chemical measurements, amplicon sequencing and metagenomics to test whether the presence of Xylophaga spp.-affected hydrogen sulfide production and wood microbial community assemblages. During a short-term experiment conducted in a deep-sea canyon, we found that wood-fall microbial communities could produce hydrogen sulfide in the absence of Xylophaga spp. The presence of wood borers had a strong impact on the microbial community composition on the wood surface but not in the wood centre, where communities were observed to be homogeneous among different samples. When wood borers were excluded, the wood centre community did not have the genetic potential to degrade cellulose or hemicellulose but could use shorter carbohydrates such as sucrose. We conclude that wood centre communities produce fermentation products that can be used by the sulfate-reducing bacteria detected near the wood surface. We thus demonstrate that microorganisms alone could establish the chemical basis essential for the recruitment of chemolithotrophic organisms in deep-sea wood falls.
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21
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Campos M, Perruchon C, Karas PA, Karavasilis D, Diez MC, Karpouzas DG. Bioaugmentation and rhizosphere-assisted biodegradation as strategies for optimization of the dissipation capacity of biobeds. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2017; 187:103-110. [PMID: 27886583 DOI: 10.1016/j.jenvman.2016.11.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 10/12/2016] [Accepted: 11/14/2016] [Indexed: 06/06/2023]
Abstract
Biobeds are on-farm biodepuration systems whose efficiency rely on their high pesticide biodegradation capacity. We evaluated two optimization strategies, bioaugmentation and/or rhizosphere-assisted biodegradation, to maximize the dissipation capacity of biobeds. Iprodione was used as a model pesticide. Its dissipation and metabolism was determined in a biobed packing material inoculated with an iprodione-degrading Arthrobacter strain C1 (bioaugmentation, treatments B+C1) and/or seeded with ryegrass (rhizosphere-assisted biodegradation, treatments B+P). The impact of those strategies on the activity and composition of the microbial community was determined. Bioaugmentation accelerated the dissipation of iprodione which was further enhanced in the bioaugmented, rhizosphere-assisted treatment (treatment B+P+C1, Half-life (DT50) = 3.4 d), compared to the non-bioaugmented, non rhizosphere-assisted control (DT50 = 9.5 d, treatment B). Bioaugmentation resulted in the earlier formation of intermediate formation of metabolites I (3,5-dichlorophenyl-carboxamide), II (3,5-dichlorophenylurea acetate) and 3,5-dichloroaniline (3,5-DCA). The latter was further dissipated by the indigenous microbial community. Acid phosphatase (AP) and β-glucosidase (GLU) were temporarily stimulated in rhizosphere-assisted treatments, whereas a stimulation of the fluorescein diacetate (FDA) hydrolytic activity in the bioaugmented treatments coincided with the hydrolysis of iprodione. q-PCR showed that changes in the abundance of alpha-proteobacteria and firmicutes was driven by the presence of rhizosphere while bioaugmentation had no significant effect.
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Affiliation(s)
- M Campos
- Biotechnological Research Center Applied to the Environment (CIBAMA), Universidad de La Frontera, Temuco, Chile
| | - C Perruchon
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Viopolis 41500, Greece
| | - P A Karas
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Viopolis 41500, Greece
| | - D Karavasilis
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Viopolis 41500, Greece
| | - M C Diez
- Chemical Engineering Department, Universidad de La Frontera, Chile
| | - D G Karpouzas
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Viopolis 41500, Greece.
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22
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Madrid F, Rubio-Bellido M, Villaverde J, Tejada M, Morillo E. Natural attenuation of fluorene and pyrene in contaminated soils and assisted with hydroxypropyl-β-cyclodextrin. Effect of co-contamination. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 571:42-49. [PMID: 27454573 DOI: 10.1016/j.scitotenv.2016.07.110] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/15/2016] [Accepted: 07/15/2016] [Indexed: 06/06/2023]
Abstract
The objectives of this study were to investigate the mutual effect of the PAHs fluorene and pyrene on their respective biodegradation and dissipation processes in an agricultural soil, and to determine the effect of hydroxypropyl-β-cyclodextrin (HPBCD), used to increase the bioavailability of PAHs, on such processes. Fluorene dissipation was primarily due to abiotic processes, although a small contribution from biodegradation was also observed. Therefore, fluorene dissipation did not increase with HPBCD and its presence did not significantly alter the dehydrogenase activity. In contrast to fluorene, pyrene dissipation depended primarily on biotic factors, with endogenous soil microorganisms capable of degrading pyrene, with large increases in dehydrogenase activity. HPBCD increased biodegradation rate of pyrene. The co-contamination of soil with both PAHs did not affect fluorene evolution, but significantly inhibited pyrene biodegradation. The different abilities of soil bacterial consortia to catabolize these PAHs are discussed. Additionally, the possibility that the abiotic loss of fluorene through volatilization had a significant effect on the microbial community biodegradation of both fluorene and pyrene is examined.
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Affiliation(s)
- F Madrid
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Apdo. 1052, 41080 Seville, Spain
| | - M Rubio-Bellido
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Apdo. 1052, 41080 Seville, Spain
| | - J Villaverde
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Apdo. 1052, 41080 Seville, Spain
| | - M Tejada
- Departamento de Cristalografía, Mineralogía y Química Agrícola, Escuela Técnica Superior de Ingeniería Agronómica, Universidad de Sevilla, Ctr. Utrera km. 1, 41013 Seville, Spain
| | - E Morillo
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Apdo. 1052, 41080 Seville, Spain.
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Singh G, Chandoha-Lee C, Zhang W, Renneckar S, Vikesland PJ, Pruden A. Biodegradation of nanocrystalline cellulose by two environmentally-relevant consortia. WATER RESEARCH 2016; 104:137-146. [PMID: 27522024 DOI: 10.1016/j.watres.2016.07.073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 07/12/2016] [Accepted: 07/29/2016] [Indexed: 06/06/2023]
Abstract
Nanocellulose is growing in popularity due to its versatile properties and applications. However, there is a void of knowledge regarding the environmental fate of nanocellulose and the response of environmental microbial communities that are historically adapted to non-nano cellulose forms. Given its distinction in terms of size and chemical and physical properties, nanocellulose could potentially resist biodegradation and/or pose a xenobiotic influence on microbial communities during wastewater treatment or in receiving environments. In this study, biodegradation of H2SO4 hydrolyzed nanocrystalline cellulose (HNC) was compared with that of microcrystalline cellulose using two distinct anaerobic cellulose-degrading microbial consortia initially sourced from anaerobic digester (AD) and wetland (W) inocula. Equivalent cellulose masses were dosed and monitored with time by measurement of liberated glucose. HNC biodegraded at slightly faster rate than microcrystalline cellulose (1st order decay constants: 0.62 ± 0.08 wk-1 for HNC versus 0.39 ± 0.05 wk-1 for microcrystalline cellulose for the AD consortium; 0.69 ± 0.04 wk-1for HNCversus 0.58 ± 0.05 wk-1 for microcrystalline cellulose for the W consortium). 16S rRNA (total bacteria) and cel48 (glycoside hydrolase gene family 48, indicative of cellulose-degrading potential) genes were observed to be more enriched in the HNC condition for both consortia. According to Illumina amplicon sequencing of 16S rRNA genes, the composition of the consortia underwent distinct shifts in concert with HNC versus microcrystalline cellulose degradation. This study demonstrates that the biodegradation of cellulose is not inhibited in the nano-size range, particularly in the crystalline form, though the microbes and pathways involved likely differ.
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Affiliation(s)
- Gargi Singh
- Department of Civil Engineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | | | - Wei Zhang
- Department of Sustainable Biomaterials, Virginia Tech, Blacksburg, VA 24060, USA; Macromolecules and Interfaces Institute, Virginia Tech, Blacksburg, VA 24060, USA
| | - Scott Renneckar
- Department of Wood Science, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Peter J Vikesland
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24060, USA
| | - Amy Pruden
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24060, USA.
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Abdelrhman KFA, Bacci G, Marras B, Nistri A, Schintu M, Ugolini A, Mengoni A. Exploring the bacterial gut microbiota of supralittoral talitrid amphipods. Res Microbiol 2016; 168:74-84. [PMID: 27531409 DOI: 10.1016/j.resmic.2016.07.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 06/24/2016] [Accepted: 07/25/2016] [Indexed: 12/22/2022]
Abstract
Talitrid amphipods (sandhoppers and beach fleas) are typical of the supralittoral zone. They are known to thrive on stranded materials, including detrital marine angiosperms and macroalgae, as well as occasional dead animals. In this work, the gut microbiota of five species of talitrid amphipods (Talitrus saltator, Talorchestia ugolinii, Sardorchestia pelecaniformis, Orchestia montagui and Orchestia stephenseni) collected in Sardinia (Italy) has been investigated through: i) metabarcoding analysis of the amplified 16S rRNA V4 region; and ii) quantification of family 48 glycosyl hydrolase genes (GHF48), involved in cellulose degradation. Results indicate that, though talitrid gut biodiversity is not directly related to taxon or sampling locality, the animals' digestive tracts may host species-specific bacterial communities. In particular, gut microbiota of O. montagui, an inhabitant of Posidonia banquettes and macro-algae mat, showed the greatest differences in taxonomic composition and the highest proportion of GHF48 genes with respect to 16S rRNA genes. These results suggest that the different talitrid species may host species-specific bacterial communities whose function could partially reflect the different microhabitats and food preferences of their host.
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Affiliation(s)
- Khaled F A Abdelrhman
- Department of Biology, University of Florence, via Madonna del Piano 6, I-50019, Sesto Fiorentino, Firenze, Italy
| | - Giovanni Bacci
- Department of Biology, University of Florence, via Madonna del Piano 6, I-50019, Sesto Fiorentino, Firenze, Italy
| | - Barbara Marras
- Department of Public Health, Molecular and Clinical Medicine, University of Cagliari, I-09124, Cagliari, Italy
| | - Annamaria Nistri
- Museum of Natural History, Zoological Section "La Specola", University of Florence, via Romana 17, I-50125, Firenze, Italy
| | - Marco Schintu
- Department of Public Health, Molecular and Clinical Medicine, University of Cagliari, I-09124, Cagliari, Italy
| | - Alberto Ugolini
- Department of Biology, University of Florence, via Madonna del Piano 6, I-50019, Sesto Fiorentino, Firenze, Italy.
| | - Alessio Mengoni
- Department of Biology, University of Florence, via Madonna del Piano 6, I-50019, Sesto Fiorentino, Firenze, Italy
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25
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Filipiak M, Sobczyk Ł, Weiner J. Fungal Transformation of Tree Stumps into a Suitable Resource for Xylophagous Beetles via Changes in Elemental Ratios. INSECTS 2016. [PMCID: PMC4931425 DOI: 10.3390/insects7020013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The elements present in dead pine stumps inhabited by larvae of wood-boring beetles (Stictoleptura rubra, Arhopalus rusticus and Chalcophora mariana) were analyzed over the initial (first 5 years; a chronosequence) stages of wood decay. The quantities of N, P, K, Ca, Mg, Fe, Zn, Mn, Cu and Na (but not S) increased with increases in the content of ergosterol (used as a proxy for the amount of fungal tissue). In fact, the amounts of P, N, K, Fe and Cu presented marked increases. These findings show that fungi stoichiometrically rearrange dead wood by importing externally occurring nutrients to decaying stumps. During the first years of wood decay, the ratios of C to other elements decrease substantially, but differently, for various elements, whereas the N:Fe, N:Cu, N:P and N:K ratios remain relatively stable. Therefore, the stoichiometric mismatch between xylophages and their food is greatly reduced. By changing the nutritional stoichiometry of dead wood, fungi create a nutritional niche for wood-eaters, and these changes enable the development of xylophages.
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26
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Hobley L, Harkins C, MacPhee CE, Stanley-Wall NR. Giving structure to the biofilm matrix: an overview of individual strategies and emerging common themes. FEMS Microbiol Rev 2015; 39:649-69. [PMID: 25907113 PMCID: PMC4551309 DOI: 10.1093/femsre/fuv015] [Citation(s) in RCA: 319] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2015] [Indexed: 01/24/2023] Open
Abstract
Biofilms are communities of microbial cells that underpin diverse processes including sewage bioremediation, plant growth promotion, chronic infections and industrial biofouling. The cells resident in the biofilm are encased within a self-produced exopolymeric matrix that commonly comprises lipids, proteins that frequently exhibit amyloid-like properties, eDNA and exopolysaccharides. This matrix fulfils a variety of functions for the community, from providing structural rigidity and protection from the external environment to controlling gene regulation and nutrient adsorption. Critical to the development of novel strategies to control biofilm infections, or the capability to capitalize on the power of biofilm formation for industrial and biotechnological uses, is an in-depth knowledge of the biofilm matrix. This is with respect to the structure of the individual components, the nature of the interactions between the molecules and the three-dimensional spatial organization. We highlight recent advances in the understanding of the structural and functional role that carbohydrates and proteins play within the biofilm matrix to provide three-dimensional architectural integrity and functionality to the biofilm community. We highlight, where relevant, experimental techniques that are allowing the boundaries of our understanding of the biofilm matrix to be extended using Escherichia coli, Staphylococcus aureus, Vibrio cholerae, and Bacillus subtilis as exemplars. Examining the structure and function of the biofilm extracellular matrix.
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Affiliation(s)
- Laura Hobley
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Catriona Harkins
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Cait E MacPhee
- James Clerk Maxwell Building, School of Physics, University of Edinburgh, Edinburgh EH9 3JZ, UK
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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Temporal and spatial constraints on community assembly during microbial colonization of wood in seawater. ISME JOURNAL 2015; 9:2657-70. [PMID: 25885564 DOI: 10.1038/ismej.2015.61] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 02/16/2015] [Accepted: 03/18/2015] [Indexed: 11/08/2022]
Abstract
Wood falls on the ocean floor form chemosynthetic ecosystems that remain poorly studied compared with features such as hydrothermal vents or whale falls. In particular, the microbes forming the base of this unique ecosystem are not well characterized and the ecology of communities is not known. Here we use wood as a model to study microorganisms that establish and maintain a chemosynthetic ecosystem. We conducted both aquaria and in situ deep-sea experiments to test how different environmental constraints structure the assembly of bacterial, archaeal and fungal communities. We also measured changes in wood lipid concentrations and monitored sulfide production as a way to detect potential microbial activity. We show that wood falls are dynamic ecosystems with high spatial and temporal community turnover, and that the patterns of microbial colonization change depending on the scale of observation. The most illustrative example was the difference observed between pine and oak wood community dynamics. In pine, communities changed spatially, with strong differences in community composition between wood microhabitats, whereas in oak, communities changed more significantly with time of incubation. Changes in community assembly were reflected by changes in phylogenetic diversity that could be interpreted as shifts between assemblies ruled by species sorting to assemblies structured by competitive exclusion. These ecological interactions followed the dynamics of the potential microbial metabolisms accompanying wood degradation in the sea. Our work showed that wood is a good model for creating and manipulating chemosynthetic ecosystems in the laboratory, and attracting not only typical chemosynthetic microbes but also emblematic macrofaunal species.
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C/N ratio drives soil actinobacterial cellobiohydrolase gene diversity. Appl Environ Microbiol 2015; 81:3016-28. [PMID: 25710367 DOI: 10.1128/aem.00067-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 02/15/2015] [Indexed: 11/20/2022] Open
Abstract
Cellulose accounts for approximately half of photosynthesis-fixed carbon; however, the ecology of its degradation in soil is still relatively poorly understood. The role of actinobacteria in cellulose degradation has not been extensively investigated despite their abundance in soil and known cellulose degradation capability. Here, the diversity and abundance of the actinobacterial glycoside hydrolase family 48 (cellobiohydrolase) gene in soils from three paired pasture-woodland sites were determined by using terminal restriction fragment length polymorphism (T-RFLP) analysis and clone libraries with gene-specific primers. For comparison, the diversity and abundance of general bacteria and fungi were also assessed. Phylogenetic analysis of the nucleotide sequences of 80 clones revealed significant new diversity of actinobacterial GH48 genes, and analysis of translated protein sequences showed that these enzymes are likely to represent functional cellobiohydrolases. The soil C/N ratio was the primary environmental driver of GH48 community compositions across sites and land uses, demonstrating the importance of substrate quality in their ecology. Furthermore, mid-infrared (MIR) spectrometry-predicted humic organic carbon was distinctly more important to GH48 diversity than to total bacterial and fungal diversity. This suggests a link between the actinobacterial GH48 community and soil organic carbon dynamics and highlights the potential importance of actinobacteria in the terrestrial carbon cycle.
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Schmidt O, Horn MA, Kolb S, Drake HL. Temperature impacts differentially on the methanogenic food web of cellulose-supplemented peatland soil. Environ Microbiol 2014; 17:720-34. [PMID: 24813682 DOI: 10.1111/1462-2920.12507] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 05/07/2014] [Indexed: 11/29/2022]
Abstract
The impact of temperature on the largely unresolved intermediary ecosystem metabolism and associated unknown microbiota that link cellulose degradation and methane production in soils of a moderately acidic (pH 4.5) fen was investigated. Supplemental [(13) C]cellulose stimulated the accumulation of propionate, acetate and carbon dioxide as well as initial methane production in anoxic peat soil slurries at 15°C and 5°C. Accumulation of organic acids at 15°C was twice as fast as that at 5°C. 16S rRNA [(13) C]cellulose stable isotope probing identified novel unclassified Bacteria (79% identity to the next cultured relative Fibrobacter succinogenes), unclassified Bacteroidetes (89% identity to Prolixibacter bellariivorans), Porphyromonadaceae, Acidobacteriaceae and Ruminococcaceae as main anaerobic degraders of cellulose-derived carbon at both 15°C and 5°C. Holophagaceae and Spirochaetaceae were more abundant at 15°C. Clostridiaceae dominated the degradation of cellulose-derived carbon only at 5°C. Methanosarcina was the dominant methanogenic taxa at both 15°C and 5°C. Relative abundance of Methanocella increased at 15°C whereas that of Methanoregula and Methanosaeta increased at 5°C. Thaumarchaeota closely related to Nitrosotalea (presently not known to grow anaerobically) were abundant at 5°C but absent at 15°C indicating that Nitrosotalea sp. might be capable of anaerobic growth at low temperatures in peat.
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Affiliation(s)
- Oliver Schmidt
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, 95440, Germany
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Soil quality: a key factor in understanding plant invasion? The case of Carpobrotus edulis (L.) N.E.Br. Biol Invasions 2013. [DOI: 10.1007/s10530-013-0531-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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31
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Song N, Cai HY, Yan ZS, Jiang HL. Cellulose degradation by one mesophilic strain Caulobacter sp. FMC1 under both aerobic and anaerobic conditions. BIORESOURCE TECHNOLOGY 2013; 131:281-7. [PMID: 23357088 DOI: 10.1016/j.biortech.2013.01.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 12/31/2012] [Accepted: 01/02/2013] [Indexed: 05/10/2023]
Abstract
Caulobacteria are presumed to be responsible for considerable mineralization of organic material in aquatic environments. In this study, a facultative, mesophilic and cellulolytic bacterium Caulobacter sp. FMC1 was isolated from sediments which were taken from a shallow freshwater lake and then enriched with amendment of submerged macrophyte for three months. This strain seemed to evolve a capacity to adapt redox-fluctuating environments, and could degrade cellulose both aerobically and anaerobically. Cellulose degradation percentages under aerobic and anaerobic conditions were approximately 27% and 10% after a 240-h incubation in liquid mediums containing 0.5% cellulose, respectively. Either cellulose or cellobiose alone was able to induce activities of endoglucanase, exoglucanase, and β-1,4-glucosidase. Interestingly, ethanol was produced as the main fermentative product under anaerobic incubation on cellulose. These results could improve our understanding about cellulose-degrading process in aquatic environments, and were also useful in optimizing cellulose bioconversion process for bioethanol production.
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Affiliation(s)
- Na Song
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, China
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Yücel M, Galand PE, Fagervold SK, Contreira-Pereira L, Le Bris N. Sulfide production and consumption in degrading wood in the marine environment. CHEMOSPHERE 2013; 90:403-409. [PMID: 22921659 DOI: 10.1016/j.chemosphere.2012.07.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 07/14/2012] [Accepted: 07/19/2012] [Indexed: 06/01/2023]
Abstract
Woody debris is known to be transported to the seas and accumulate on the seafloor, however, little is known on the consequences of its degradation in the marine environment. In this study we monitored the degradation product sulfide with Au/Hg voltammetric microelectrodes on the surface and interior of an experimentally immersed wood for 200 d. After 5 weeks of immersion, the interior became sulfidic, and steady-state conditions were established after 13 weeks with sulfide concentration reaching about 300 μM. Although sulfide was briefly detected at the surface of wood, its concentration remained lower than 20 μM, indicating that this compound was effectively oxidized within the substrate. Fitting these data to a kinetic model lead to an estimated microbial sulfide production rate in the range of 19-28 μM d(-1) at steady state. As much as 24 μM d(-1) nitrate could be consumed by this process in the steady-state period. Before the establishment of the steady state conditions, steep fluctuations in sulfide concentration (between 1mM and several μM) were observed in the wood interior. This study is the first to document the temporal dynamics of this unsteady process, characterized by fast sulfide fluctuation and consumption. Our results point to the complex mechanisms driving the dynamics of wood biogeochemical transformations, and reveal the capacity of woody debris to generate sulfidic conditions and act as a possible sink for oxygen and nitrate in the marine environment.
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Affiliation(s)
- Mustafa Yücel
- UPMC, Univ Paris 06, LECOB, Observatoire Océanologique, Banyuls-sur-mer, France.
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Paenibacillus xylaniclasticus sp. nov., a xylanolytic-cellulolytic bacterium isolated from sludge in an anaerobic digester. J Microbiol 2012; 50:394-400. [PMID: 22752902 DOI: 10.1007/s12275-012-1480-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 03/11/2012] [Indexed: 10/28/2022]
Abstract
A mesophilic, facultative, anaerobic, xylanolytic-cellulolytic bacterium, TW1(T), was isolated from sludge in an anaerobic digester fed with pineapple waste. Cells stained Gram-positive, were spore-forming, and had the morphology of straight to slightly curved rods. Growth was observed in the temperature range of 30 to 50°C (optimum 37°C) and the pH range of 6.0 to 7.5 (optimum pH 7.0) under aerobic and anaerobic conditions. The strain contained meso-diaminopimelic acid in the cell-wall peptidoglycan. The predominant isoprenoid quinone was menaquinone with seven isoprene units (MK-7). Anteiso-C(15:0), iso-C(16:0), anteiso-C(17:0), and C(16:0) were the predominant cellular fatty acids. The G+C content of the DNA was 49.5 mol%. A phylogenetic analysis based on 16S rRNA showed that strain TW1(T) belonged within the genus Paenibacillus and was closely related to Paenibacillus cellulosilyticus LMG 22232(T), P. curdlanolyticus KCTC 3759(T), and P. kobensis KCTC 3761(T) with 97.7, 97.5, and 97.3% sequence similarity, respectively. The DNA-DNA hybridization values between the isolate and type strains of P. cellulosilyticus LMG 22232(T), P. curdlanolyticus KCTC 3759(T), and P. kobensis KCTC 3761(T) were found to be 18.6, 18.3, and 18.0%, respectively. The protein and xylanase patterns of strain TW1(T) were quite different from those of the type strains of closely related Paenibacillus species. On the basis of DNA-DNA relatedness and phenotypic analyses, phylogenetic data and the enzymatic pattern presented in this study, strain TW1(T) should be classified as a novel species of the genus Paenibacillus, for which the name Paenibacillus xylaniclasticus sp. nov. is proposed. The type strain is TW1(T) (=NBRC 106381(T) =KCTC 13719(T) =TISTR 1914(T)).
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Hattori T, Ogata M, Kameshima Y, Totani K, Nikaido M, Nakamura T, Koshino H, Usui T. Enzymatic synthesis of cellulose II-like substance via cellulolytic enzyme-mediated transglycosylation in an aqueous medium. Carbohydr Res 2012; 353:22-6. [PMID: 22533921 DOI: 10.1016/j.carres.2012.03.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2011] [Revised: 03/05/2012] [Accepted: 03/16/2012] [Indexed: 11/17/2022]
Abstract
The enzymatic synthesis of cellulose-like substance via a non-biosynthetic pathway has been achieved by transglycosylation in an aqueous system of the corresponding substrate, cellotriose for cellulolytic enzyme endo-acting endoglucanase I (EG I) from Hypocrea jecorina. A significant amount of water-insoluble product precipitated out from the reaction system. MALDI-TOF mass analysis showed that the resulting precipitate had a degree of polymerization (DP) of up to 16 from cellotriose. Solid-state (13)C NMR spectrum of the resulting water-insoluble product revealed that all carbon resonance lines were assigned to two kinds of anhydroglucose residues in the corresponding structure of cellulose II. X-ray diffraction (XRD) measurement as well as (13)C NMR analysis showed that the crystal structure corresponds to cellulose II with a high degree of crystallinity. We propose the multiple oligomers form highly crystalline cellulose II as a result of self-assembly via oligomer-oligomer interaction when they precipitate.
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Affiliation(s)
- Takeshi Hattori
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga ward, Shizuoka 422-8529, Japan
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Hii KL, Yeap SP, Mashitah MD. Cellulase production from palm oil mill effluent in Malaysia: Economical and technical perspectives. Eng Life Sci 2011. [DOI: 10.1002/elsc.201000228] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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Young JM, Leschine SB, Reguera G. Reversible control of biofilm formation by Cellulomonas spp. in response to nitrogen availability. Environ Microbiol 2011; 14:594-604. [PMID: 21951594 DOI: 10.1111/j.1462-2920.2011.02596.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jenna M Young
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
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Zhou J, Shi P, Huang H, Cao Y, Meng K, Yang P, Zhang R, Chen X, Yao B. A new α-galactosidase from symbiotic Flavobacterium sp. TN17 reveals four residues essential for α-galactosidase activity of gastrointestinal bacteria. Appl Microbiol Biotechnol 2010; 88:1297-309. [DOI: 10.1007/s00253-010-2809-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 07/06/2010] [Accepted: 07/30/2010] [Indexed: 10/19/2022]
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38
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Scharf ME, Kovaleva ES, Jadhao S, Campbell JH, Buchman GW, Boucias DG. Functional and translational analyses of a beta-glucosidase gene (glycosyl hydrolase family 1) isolated from the gut of the lower termite Reticulitermes flavipes. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2010; 40:611-20. [PMID: 20558291 DOI: 10.1016/j.ibmb.2010.06.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Revised: 06/04/2010] [Accepted: 06/07/2010] [Indexed: 05/25/2023]
Abstract
This research focused on digestive beta-glucosidases from glycosyl hydrolase family (GHF) 1 from the gut of the lower termite Reticulitermes flavipes. In preceding studies on R. flavipes, we characterized beta-glucosidase activity across the gut and its inhibition by carbohydrate-based inhibitors, and subsequently we identified two partial beta-glucosidase cDNA sequences from a host gut cDNA library. Here, we report on the full-length cDNA sequence for one of the R. flavipes beta-glucosidases (RfBGluc-1), the expression of its mRNA in the salivary gland and foregut, the production of recombinant protein using a baculovirus-insect expression system, optimal recombinant substrate specificity profiles and parameters, and significant inhibition by the established beta-glucosidase inhibitor cellobioimidazole. We also report the partial cDNA sequence for a second gut beta-glucosidase (RfBGluc-2), and show that like RfBGluc-1 its mRNA is localized mainly in the salivary gland. Other results for RfBGluc-1 showing activity against laminaribose, a component of microbial cell walls, suggest that RfBGluc-1 may serve dual functions in cellulose digestion and immunity. These findings provide important information that will enable the testing of hypotheses related to collaborative host-symbiont lignocellulose digestion, and that contributes to the development of next-generation termiticides and novel biocatalyst cocktails for use in biomass-to-bioethanol applications.
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Affiliation(s)
- Michael E Scharf
- Entomology and Nematology Department, University of Florida, PO Box 110620, Gainesville, FL 32611-0620, USA.
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39
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Abstract
Four strains of anaerobic nitrogen-fixing, cellulose-fermenting bacteria were isolated in pure culture from freshwater mud and soil. Nitrogenase activity was demonstrated in these strains and also in several previously described anaerobic cellulolytic bacteria isolated from various natural environments. These are the first anaerobic bacteria known to use cellulose as an energy source for nitrogen fixation. Because cellulose is a plant polysaccharide that abounds in nature, these results raise the possibility that nitrogen-fixing, cellulose-fermenting bacteria may be widespread and thus play a major role in carbon and nitrogen cycling.
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40
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Wheeler MM, Tarver MR, Coy MR, Scharf ME. Characterization of four esterase genes and esterase activity from the gut of the termite Reticulitermes flavipes. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2010; 73:30-48. [PMID: 19802899 DOI: 10.1002/arch.20333] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Four esterase genes and general esterase activity were investigated in the gut of the termite Reticulitermes flavipes. Two genes (RfEst1 and RfEst2) share significant translated identity with a number of insect JH esterases. The two remaining genes (RfEst3 and RfEst4) apparently code for much shorter proteins with similarity to fungal phenolic acid esterases involved in hemicellulose solubilization. All four genes showed consistently high midgut expression. This result was further supported by colorimetric activity assays and Native polyacrylamide gel electrophoresis, which showed significant esterase activity and a number of isoforms in the midgut. The greatest esterase activity and isoform composition were detected when alpha-naphthyl propionate was used as a substrate. Moreover, esterase activity and diverse isoforms were present in gut mitochondrial, microsomal, and cytosolic sub-cellular protein fractions, as well as in the hindgut lumen. These findings reveal an agreement between gut esterase gene expression and activity distributions, and support the idea that R. flavipes gut esterase activity is host (not symbiont)-derived. In addition, these findings support the hypotheses that termite gut esterases may play important roles in lignocellulose digestion and caste differentiation. This study provides important baseline data that will assist ongoing functional-genomic efforts to identify novel genes with roles in semiochemical, hormone, and lignocellulose processing in the termite gut.
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Affiliation(s)
- Marsha M Wheeler
- Entomology and Nematology Department, University of Florida, Gainesville, FL 32611-0620, USA
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41
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Davis JR, Sello JK. Regulation of genes in Streptomyces bacteria required for catabolism of lignin-derived aromatic compounds. Appl Microbiol Biotechnol 2009; 86:921-9. [DOI: 10.1007/s00253-009-2358-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Revised: 11/10/2009] [Accepted: 11/11/2009] [Indexed: 10/20/2022]
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42
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Palacios C, Zbinden M, Pailleret M, Gaill F, Lebaron P. Highly similar prokaryotic communities of sunken wood at shallow and deep-sea sites across the oceans. MICROBIAL ECOLOGY 2009; 58:737-752. [PMID: 19547939 DOI: 10.1007/s00248-009-9538-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Accepted: 05/15/2009] [Indexed: 05/28/2023]
Abstract
With an increased appreciation of the frequency of their occurrence, large organic falls such as sunken wood and whale carcasses have become important to consider in the ecology of the oceans. Organic-rich deep-sea falls may play a major role in the dispersal and evolution of chemoautotrophic communities at the ocean floor, and chemosynthetic symbiotic, free-living, and attached microorganisms may drive the primary production at these communities. However, little is known about the microbiota thriving in and around organic falls. Our aim was to investigate and compare free-living and attached communities of bacteria and archaea from artificially immersed and naturally sunken wood logs with varying characteristics at several sites in the deep sea and in shallow water to address basic questions on the microbial ecology of sunken wood. Multivariate indirect ordination analyses of capillary electrophoresis single-stranded conformation polymorphisms (CE-SSCP) fingerprinting profiles demonstrated high similarity of bacterial and archaeal assemblages present in timbers and logs situated at geographically distant sites and at different depths of immersion. This similarity implies that wood falls harbor a specialized microbiota as observed in other ecosystems when the same environmental conditions reoccur. Scanning and transmission electron microscopy observations combined with multivariate direct gradient analysis of Bacteria CE-SSCP profiles demonstrate that type of wood (hard vs. softwood), and time of immersion are important in structuring sunken wood bacterial communities. Archaeal populations were present only in samples with substantial signs of decay, which were also more similar in their bacterial assemblages, providing indirect evidence of temporal succession in the microbial communities that develop in and around wood falls.
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Affiliation(s)
- Carmen Palacios
- Laboratoire ARAGO, Observatoire Océanologique de Banyuls-sur-mer (OOB), Université Pierre et Marie Curie-Paris6, Banyuls-sur-mer, BP44, 66650, France.
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Abstract
Frankly, I was surprised to receive an invitation to write a prefatory chapter for the Annual Review of Microbiology. I have read several such chapters written by outstanding researchers, many of whom I know and admire. I did not think I belonged to such a preeminent group. In my view, my contributions to the physiology and biochemistry of anaerobic thermophilic bacteria and, more lately, to anaerobic fungi are modest compared to the contribution made by other authors of prefatory chapters. I am honored to write about my life and my work, and I hope that those who read this chapter will sense how exciting and rewarding they have been.
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Affiliation(s)
- Lars G Ljungdahl
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, Georgia 30602, USA.
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Geib SM, Jimenez-Gasco MDM, Carlson JE, Tien M, Hoover K. Effect of host tree species on cellulase activity and bacterial community composition in the gut of larval Asian longhorned beetle. ENVIRONMENTAL ENTOMOLOGY 2009; 38:686-99. [PMID: 19508777 DOI: 10.1603/022.038.0320] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Anoplophora glabripennis, the Asian longhorned beetle, is a wood-boring insect that can develop in a wide range of healthy deciduous hosts and requires gut microbes to aid in wood degradation and digestion. Here we show that larval A. glabripennis harbor a diverse gut bacterial community, and this community can be extremely variable when reared in different host trees. A. glabripennis reared in a preferred host (Acer saccharum) had the highest gut bacterial diversity compared with larvae reared either in a secondary host (Quercus palustris), a resistant host (Pyrus calleryana), or on artificial diet. The gut microbial community of larval A. glabripennis collected from field populations on Brooklyn, NY, showed the highest degree of complexity among all samples in this study. Overall, when larvae fed on a preferred host, they harbored a broad diversity of gut bacteria spanning the alpha-, beta-, gamma-Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Cellulase activities (beta-1,4-endoglucanase, beta-1,4-exoglucanase, and beta-1,4-glucosidase) in the guts of larvae fed in a preferred host (A. saccharum) or a secondary host (Q. palustris) were significantly higher than that of artificial diet fed larvae. Larvae that fed on wood from a resistant host (P. calleryana) showed suppressed total gut cellulase activity. Results show that the host tree can impact both gut microbial community complexity and cellulase activity in A. glabripennis.
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Affiliation(s)
- Scott M Geib
- Department of Entomology, The Pennsylvania State University, University Park, PA 16802, USA
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Béguin P, Gilkes NR, Kilburn DG, Miller RC, O'neill GP, Warren RAJ. Cloning of Cellulase Genes. Crit Rev Biotechnol 2008. [DOI: 10.3109/07388558709113595] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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46
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Wiegel J, Ljungdahl LG, Demain AL. The Importance of Thermophilic Bacteria in Biotechnology. Crit Rev Biotechnol 2008. [DOI: 10.3109/07388558509150780] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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47
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Sinsabaugh RL, Lauber CL, Weintraub MN, Ahmed B, Allison SD, Crenshaw C, Contosta AR, Cusack D, Frey S, Gallo ME, Gartner TB, Hobbie SE, Holland K, Keeler BL, Powers JS, Stursova M, Takacs-Vesbach C, Waldrop MP, Wallenstein MD, Zak DR, Zeglin LH. Stoichiometry of soil enzyme activity at global scale. Ecol Lett 2008; 11:1252-1264. [DOI: 10.1111/j.1461-0248.2008.01245.x] [Citation(s) in RCA: 1254] [Impact Index Per Article: 78.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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48
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Ljungdahl LG. The cellulase/hemicellulase system of the anaerobic fungus Orpinomyces PC-2 and aspects of its applied use. Ann N Y Acad Sci 2008; 1125:308-21. [PMID: 18378601 DOI: 10.1196/annals.1419.030] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Anaerobic fungi, first described in 1975 by Orpin, live in close contact with bacteria and other microorganisms in the rumen and caecum of herbivorous animals, where they digest ingested plant food. Seventeen distinct anaerobic fungi belonging to five different genera have been described. They have been found in at least 50 different herbivorous animals. Anaerobic fungi do not possess mitochondria, but instead have hydrogenosomes, which form hydrogen and carbon dioxide from pyruvate and malate during fermentation of carbohydrates. In addition, they are very oxygen- and temperature-sensitive, and their DNA has an unusually high AT content of from 72 to 87 mol%. My initial reason for studying anaerobic fungi was because they solubilize lignocellulose and produce all enzymes needed to efficiently hydrolyze cellulose and hemicelluloses. Although some of these enzymes are found free in the medium, most of them are associated with cellulosomal and polycellulosomal complexes, in which the enzymes are attached through fungal dockerins to scaffolding proteins; this is similar to what has been found for cellulosomes from anaerobic bacteria. Although cellulosomes from anaerobic fungi share many properties with cellulosomes of anaerobic cellulolytic bacteria and have comparable structures, their structures differ in their amino acid sequences. I discuss some features of the cellulosome of the anaerobic fungus Orpinomyces sp. PC-2 and some possible uses of its enzymes in industrial settings.
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Affiliation(s)
- Lars G Ljungdahl
- Department of Biochemistry and Molecular Biology, Fred C. Davison Life Sciences Complex, University of Georgia, Athens, GA 30602-7229, USA.
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49
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JEPSON PC, CROFT BA, PRATT GE. Test systems to determine the ecological risks posed by toxin release from Bacillus thuringiensis genes in crop plants. Mol Ecol 2008. [DOI: 10.1111/j.1365-294x.1994.tb00049.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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50
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Isolation, purification, and enzymatic activity of cellulase components of the fungus Aspergillus terreus. Chem Nat Compd 2007. [DOI: 10.1007/s10600-007-0199-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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