- home
- Advanced Search
Filters
Clear AllYear range
-chevron_right GOSource
Organization
- Energy Research
- FR
- Energy Research
- FR
description Publicationkeyboard_double_arrow_right Article , Journal 2019Publisher:Elsevier BV Yunfu Gu; Yunfu Gu; Nona R. Chiariello; Tong Yuan; Audrey Niboyet; Mengting Yuan; Shikui Dong; Sihang Yang; Qiaoshu Zheng; Jizhong Zhou; Jizhong Zhou; Jizhong Zhou; Zhou Shi; Jessica L. M. Gutknecht; Xingyu Ma; Kathryn M. Docherty; Christopher B. Field; Bruce A. Hungate; Xavier Le Roux; Yunfeng Yang;pmid: 30586832
The continuously increasing concentration of atmospheric CO2 has considerably altered ecosystem functioning. However, few studies have examined the long-term (i.e. over a decade) effect of elevated CO2 on soil microbial communities. Using 16S rRNA gene amplicons and a GeoChip microarray, we investigated soil microbial communities from a Californian annual grassland after 14 years of experimentally elevated CO2 (275 ppm higher than ambient). Both taxonomic and functional gene compositions of the soil microbial community were modified by elevated CO2. There was decrease in relative abundance for taxa with higher ribosomal RNA operon (rrn) copy number under elevated CO2, which is a functional trait that responds positively to resource availability in culture. In contrast, taxa with lower rrn copy number were increased by elevated CO2. As a consequence, the abundance-weighted average rrn copy number of significantly changed OTUs declined from 2.27 at ambient CO2 to 2.01 at elevated CO2. The nitrogen (N) fixation gene nifH and the ammonium-oxidizing gene amoA significantly decreased under elevated CO2 by 12.6% and 6.1%, respectively. Concomitantly, nitrifying enzyme activity decreased by 48.3% under elevated CO2, albeit this change was not significant. There was also a substantial but insignificant decrease in available soil N, with both nitrate (NO3-) (-27.4%) and ammonium (NH4+) (-15.4%) declining. Further, a large number of microbial genes related to carbon (C) degradation were also affected by elevated CO2, whereas those related to C fixation remained largely unchanged. The overall changes in microbial communities and soil N pools induced by long-term elevated CO2 suggest constrained microbial N decomposition, thereby slowing the potential maximum growth rate of the microbial community.
The Science of The T... arrow_drop_down The Science of The Total EnvironmentArticle . 2019 . Peer-reviewedLicense: Elsevier TDMData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1016/j.scitotenv.2018.10.353&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routesbronze 42 citations 42 popularity Top 10% influence Average impulse Top 10% Powered by BIP!
more_vert The Science of The T... arrow_drop_down The Science of The Total EnvironmentArticle . 2019 . Peer-reviewedLicense: Elsevier TDMData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1016/j.scitotenv.2018.10.353&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Journal 2012Publisher:Springer Science and Business Media LLC Raphael Lamed; Yue Huang; Bernard Henrissat; Ilya Borovok; Christopher L. Hemme; Jizhong Zhou; Pedro M. Coutinho; Edward A. Bayer; Bareket Dassa;Abstract Background Microbial degradation of plant cell walls and its conversion to sugars and other byproducts is a key step in the carbon cycle on Earth. In order to process heterogeneous plant-derived biomass, specialized anaerobic bacteria use an elaborate multi-enzyme cellulosome complex to synergistically deconstruct cellulosic substrates. The cellulosome was first discovered in the cellulolytic thermophile, Clostridium thermocellum, and much of our knowledge of this intriguing type of protein composite is based on the cellulosome of this environmentally and biotechnologically important bacterium. The recently sequenced genome of the cellulolytic mesophile, Acetivibrio cellulolyticus, allows detailed comparison of the cellulosomes of these two select cellulosome-producing bacteria. Results Comprehensive analysis of the A. cellulolyticus draft genome sequence revealed a very sophisticated cellulosome system. Compared to C. thermocellum, the cellulosomal architecture of A. cellulolyticus is much more extensive, whereby the genome encodes for twice the number of cohesin- and dockerin-containing proteins. The A. cellulolyticus genome has thus evolved an inflated number of 143 dockerin-containing genes, coding for multimodular proteins with distinctive catalytic and carbohydrate-binding modules that play critical roles in biomass degradation. Additionally, 41 putative cohesin modules distributed in 16 different scaffoldin proteins were identified in the genome, representing a broader diversity and modularity than those of Clostridium thermocellum. Although many of the A. cellulolyticus scaffoldins appear in unconventional modular combinations, elements of the basic structural scaffoldins are maintained in both species. In addition, both species exhibit similarly elaborate cell-anchoring and cellulosome-related gene- regulatory elements. Conclusions This work portrays a particularly intricate, cell-surface cellulosome system in A. cellulolyticus and provides a blueprint for examining the specific roles of the various cellulosomal components in the degradation of complex carbohydrate substrates of the plant cell wall by the bacterium.
add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1186/1471-2164-13-210&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 59 citations 59 popularity Top 10% influence Top 10% impulse Top 10% Powered by BIP!
more_vert add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1186/1471-2164-13-210&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Journal 2019 United StatesPublisher:Wiley Xingyu Ma; Jessica Gutknecht; N. R. Chiariello; Audrey Niboyet; Audrey Niboyet; Christopher B. Field; Bruce A. Hungate; Jizhong Zhou; Jizhong Zhou; Jizhong Zhou; Yunfeng Yang; Qiaoshu Zheng; Mengting Yuan; Sihang Yang; Xavier Le Roux; Kathryn M. Docherty;doi: 10.1111/gcb.14852
pmid: 31562826
AbstractFire is a crucial event regulating the structure and functioning of many ecosystems. Yet few studies have focused on how fire affects taxonomic and functional diversities of soil microbial communities, along with changes in plant communities and soil carbon (C) and nitrogen (N) dynamics. Here, we analyze these effects in a grassland ecosystem 9 months after an experimental fire at the Jasper Ridge Global Change Experiment site in California, USA. Fire altered soil microbial communities considerably, with community assembly process analysis showing that environmental selection pressure was higher in burned sites. However, a small subset of highly connected taxa was able to withstand the disturbance. In addition, fire decreased the relative abundances of most functional genes associated with C degradation and N cycling, implicating a slowdown of microbial processes linked to soil C and N dynamics. In contrast, fire stimulated above‐ and belowground plant growth, likely enhancing plant–microbe competition for soil inorganic N, which was reduced by a factor of about 2. To synthesize those findings, we performed structural equation modeling, which showed that plants but not microbial communities were responsible for significantly higher soil respiration rates in burned sites. Together, our results demonstrate that fire ‘reboots’ the grassland ecosystem by differentially regulating plant and soil microbial communities, leading to significant changes in soil C and N dynamics.
Global Change Biolog... arrow_drop_down Global Change BiologyArticle . 2019 . Peer-reviewedLicense: Wiley Online Library User AgreementData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1111/gcb.14852&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen hybrid 49 citations 49 popularity Top 1% influence Average impulse Top 10% Powered by BIP!
more_vert Global Change Biolog... arrow_drop_down Global Change BiologyArticle . 2019 . Peer-reviewedLicense: Wiley Online Library User AgreementData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1111/gcb.14852&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Journal 2017 Russian Federation, United StatesPublisher:Wiley Nianpeng He; Yuan Liu; Jizhong Zhou; Jizhong Zhou; Jizhong Zhou; Jing Tian; Qun Gao; Qun Gao; Guirui Yu; Evgenia Blagodatskaya; Yakov Kuzyakov; Lauren Hale; Shuli Niu;Abstract Bacteria are one of the most abundant and diverse groups of micro‐organisms and mediate many critical terrestrial ecosystem processes. Despite the crucial ecological role of bacteria, our understanding of their large‐scale biogeography patterns across forests, and the processes that determine these patterns lags significantly behind that of macroorganisms. Here, we evaluated the geographic distributions of bacterial diversity and their driving factors across nine latitudinal forests along a 3,700‐km north–south transect in eastern China, using high‐throughput 16S rRNA gene sequencing. Four of 32 phyla detected were dominant: Acidobacteria, Actinobacteria, Alphaproteobacteria and Chloroflexi (relative abundance > 5%). Significant increases in bacterial richness and phylogenetic diversity were observed for temperate forests compared with subtropical or tropical forests. The soil organic matter (SOM) mineralisation rate (SOMmin, an index of SOM availability) explained the largest significant variations in bacterial richness. Variation partition analysis revealed that the bacterial community structure was closely correlated with environmental variables and geographic distance, which together explained 80.5% of community variation. Among all environmental factors, climatic features (MAT and MAP) were the best predictors of the bacterial community structure, whereas soil pH and SOMmin emerged as the most important edaphic drivers of the bacterial community structure. Plant functional traits (community weighted means of litter N content) and diversity resulted in weak but significant correlations with the bacterial community structure. Our findings provide new evidence of bacterial biogeography patterns from tropical to cold temperate forests. Additionally, the results indicated a close linkage among soil bacterial diversity, climate and SOM decomposition, which is critical for predicting continental‐scale responses under future climate change scenarios and promoting sustainable forest ecosystem services. A plain language summary is available for this article.
Functional Ecology arrow_drop_down Functional EcologyArticle . 2017 . Peer-reviewedLicense: Wiley Online Library User AgreementData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1111/1365-2435.12952&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen bronze 121 citations 121 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!
more_vert Functional Ecology arrow_drop_down Functional EcologyArticle . 2017 . Peer-reviewedLicense: Wiley Online Library User AgreementData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1111/1365-2435.12952&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2023Publisher:Wiley Mengmeng Wang; Xin Sun; Baichuan Cao; Nona R. Chiariello; Kathryn M. Docherty; Christopher B. Field; Qun Gao; Jessica L. M. Gutknecht; Xue Guo; Genhe He; Bruce A. Hungate; Jiesi Lei; Audrey Niboyet; Xavier Le Roux; Zhou Shi; Wensheng Shu; Mengting Yuan; Jizhong Zhou; Yunfeng Yang;doi: 10.1111/gcb.16811
pmid: 37317051
AbstractGlobal climate models predict that the frequency and intensity of precipitation events will increase in many regions across the world. However, the biosphere‐climate feedback to elevated precipitation (eP) remains elusive. Here, we report a study on one of the longest field experiments assessing the effects of eP, alone or in combination with other climate change drivers such as elevated CO2 (eCO2), warming and nitrogen deposition. Soil total carbon (C) decreased after a decade of eP treatment, while plant root production decreased after 2 years. To explain this asynchrony, we found that the relative abundances of fungal genes associated with chitin and protein degradation increased and were positively correlated with bacteriophage genes, suggesting a potential viral shunt in C degradation. In addition, eP increased the relative abundances of microbial stress tolerance genes, which are essential for coping with environmental stressors. Microbial responses to eP were phylogenetically conserved. The effects of eP on soil total C, root production, and microbes were interactively affected by eCO2. Collectively, we demonstrate that long‐term eP induces soil C loss, owing to changes in microbial community composition, functional traits, root production, and soil moisture. Our study unveils an important, previously unknown biosphere‐climate feedback in Mediterranean‐type water‐limited ecosystems, namely how eP induces soil C loss via microbe‐plant–soil interplay.
Global Change Biolog... arrow_drop_down Global Change BiologyArticle . 2023 . Peer-reviewedLicense: Wiley Online Library User AgreementData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1111/gcb.16811&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen bronze 8 citations 8 popularity Top 10% influence Average impulse Top 10% Powered by BIP!
more_vert Global Change Biolog... arrow_drop_down Global Change BiologyArticle . 2023 . Peer-reviewedLicense: Wiley Online Library User AgreementData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1111/gcb.16811&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Journal 2010 United StatesPublisher:American Society for Microbiology Safiyh Taghavi; Housna Mouttaki; Liyou Wu; Alla Lapidus; Jonathan R. Mielenz; Elizabeth Saunders; Joy D. Van Nostrand; Nikos C. Kyrpides; Matthew W. Fields; Bradley S. Stevenson; Bernard Henrissat; Sam Pitluck; Michael E. Himmel; Raymond L. Huhnke; Zhili He; Cliff Han; Tijana Glavina del Rio; Michael J. McInerney; Qiang He; Jizhong Zhou; Lynne Goodwin; Gengxin Zhang; Natalia Mikhailova; Aijie Wang; Hope Tice; Christopher W. Schadt; Yunfeng Yang; Daniel van der Lelie; Yong-Jin Lee; Defeng Xing; Shi You Ding; Susan Lucas; Ralph S. Tanner; Miriam Land; Loren Hauser; Thomas Brettin; Thomas Brettin; Christopher L. Hemme; Adam P. Arkin; Hailiang Dong; Edward M. Rubin; Nanqi Ren; Juergen Wiegel; Alex Copeland; John C. Detter; Paul A. Lawson; Lee R. Lynd;ABSTRACT Modern methods to develop microbe-based biomass conversion processes require a system-level understanding of the microbes involved. Clostridium species have long been recognized as ideal candidates for processes involving biomass conversion and production of various biofuels and other industrial products. To expand the knowledge base for clostridial species relevant to current biofuel production efforts, we have sequenced the genomes of 20 species spanning multiple genera. The majority of species sequenced fall within the class III cellulosome-encoding Clostridium and the class V saccharolytic Thermoanaerobacteraceae . Species were chosen based on representation in the experimental literature as model organisms, ability to degrade cellulosic biomass either by free enzymes or by cellulosomes, ability to rapidly ferment hexose and pentose sugars to ethanol, and ability to ferment synthesis gas to ethanol. The sequenced strains significantly increase the number of noncommensal/nonpathogenic clostridial species and provide a key foundation for future studies of biomass conversion, cellulosome composition, and clostridial systems biology.
Journal of Bacteriol... arrow_drop_down Journal of BacteriologyArticle . 2010 . Peer-reviewedLicense: ASM Journals Non-Commercial TDMData sources: CrossrefUniversity of Oklahoma/Oklahoma State University: SHAREOK RepositoryArticle . 2015Data sources: Bielefeld Academic Search Engine (BASE)add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1128/jb.01064-10&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen bronze 76 citations 76 popularity Top 10% influence Top 10% impulse Top 10% Powered by BIP!
more_vert Journal of Bacteriol... arrow_drop_down Journal of BacteriologyArticle . 2010 . Peer-reviewedLicense: ASM Journals Non-Commercial TDMData sources: CrossrefUniversity of Oklahoma/Oklahoma State University: SHAREOK RepositoryArticle . 2015Data sources: Bielefeld Academic Search Engine (BASE)add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1128/jb.01064-10&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu
description Publicationkeyboard_double_arrow_right Article , Journal 2019Publisher:Elsevier BV Yunfu Gu; Yunfu Gu; Nona R. Chiariello; Tong Yuan; Audrey Niboyet; Mengting Yuan; Shikui Dong; Sihang Yang; Qiaoshu Zheng; Jizhong Zhou; Jizhong Zhou; Jizhong Zhou; Zhou Shi; Jessica L. M. Gutknecht; Xingyu Ma; Kathryn M. Docherty; Christopher B. Field; Bruce A. Hungate; Xavier Le Roux; Yunfeng Yang;pmid: 30586832
The continuously increasing concentration of atmospheric CO2 has considerably altered ecosystem functioning. However, few studies have examined the long-term (i.e. over a decade) effect of elevated CO2 on soil microbial communities. Using 16S rRNA gene amplicons and a GeoChip microarray, we investigated soil microbial communities from a Californian annual grassland after 14 years of experimentally elevated CO2 (275 ppm higher than ambient). Both taxonomic and functional gene compositions of the soil microbial community were modified by elevated CO2. There was decrease in relative abundance for taxa with higher ribosomal RNA operon (rrn) copy number under elevated CO2, which is a functional trait that responds positively to resource availability in culture. In contrast, taxa with lower rrn copy number were increased by elevated CO2. As a consequence, the abundance-weighted average rrn copy number of significantly changed OTUs declined from 2.27 at ambient CO2 to 2.01 at elevated CO2. The nitrogen (N) fixation gene nifH and the ammonium-oxidizing gene amoA significantly decreased under elevated CO2 by 12.6% and 6.1%, respectively. Concomitantly, nitrifying enzyme activity decreased by 48.3% under elevated CO2, albeit this change was not significant. There was also a substantial but insignificant decrease in available soil N, with both nitrate (NO3-) (-27.4%) and ammonium (NH4+) (-15.4%) declining. Further, a large number of microbial genes related to carbon (C) degradation were also affected by elevated CO2, whereas those related to C fixation remained largely unchanged. The overall changes in microbial communities and soil N pools induced by long-term elevated CO2 suggest constrained microbial N decomposition, thereby slowing the potential maximum growth rate of the microbial community.
The Science of The T... arrow_drop_down The Science of The Total EnvironmentArticle . 2019 . Peer-reviewedLicense: Elsevier TDMData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1016/j.scitotenv.2018.10.353&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routesbronze 42 citations 42 popularity Top 10% influence Average impulse Top 10% Powered by BIP!
more_vert The Science of The T... arrow_drop_down The Science of The Total EnvironmentArticle . 2019 . Peer-reviewedLicense: Elsevier TDMData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1016/j.scitotenv.2018.10.353&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Journal 2012Publisher:Springer Science and Business Media LLC Raphael Lamed; Yue Huang; Bernard Henrissat; Ilya Borovok; Christopher L. Hemme; Jizhong Zhou; Pedro M. Coutinho; Edward A. Bayer; Bareket Dassa;Abstract Background Microbial degradation of plant cell walls and its conversion to sugars and other byproducts is a key step in the carbon cycle on Earth. In order to process heterogeneous plant-derived biomass, specialized anaerobic bacteria use an elaborate multi-enzyme cellulosome complex to synergistically deconstruct cellulosic substrates. The cellulosome was first discovered in the cellulolytic thermophile, Clostridium thermocellum, and much of our knowledge of this intriguing type of protein composite is based on the cellulosome of this environmentally and biotechnologically important bacterium. The recently sequenced genome of the cellulolytic mesophile, Acetivibrio cellulolyticus, allows detailed comparison of the cellulosomes of these two select cellulosome-producing bacteria. Results Comprehensive analysis of the A. cellulolyticus draft genome sequence revealed a very sophisticated cellulosome system. Compared to C. thermocellum, the cellulosomal architecture of A. cellulolyticus is much more extensive, whereby the genome encodes for twice the number of cohesin- and dockerin-containing proteins. The A. cellulolyticus genome has thus evolved an inflated number of 143 dockerin-containing genes, coding for multimodular proteins with distinctive catalytic and carbohydrate-binding modules that play critical roles in biomass degradation. Additionally, 41 putative cohesin modules distributed in 16 different scaffoldin proteins were identified in the genome, representing a broader diversity and modularity than those of Clostridium thermocellum. Although many of the A. cellulolyticus scaffoldins appear in unconventional modular combinations, elements of the basic structural scaffoldins are maintained in both species. In addition, both species exhibit similarly elaborate cell-anchoring and cellulosome-related gene- regulatory elements. Conclusions This work portrays a particularly intricate, cell-surface cellulosome system in A. cellulolyticus and provides a blueprint for examining the specific roles of the various cellulosomal components in the degradation of complex carbohydrate substrates of the plant cell wall by the bacterium.
add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1186/1471-2164-13-210&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 59 citations 59 popularity Top 10% influence Top 10% impulse Top 10% Powered by BIP!
more_vert add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1186/1471-2164-13-210&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Journal 2019 United StatesPublisher:Wiley Xingyu Ma; Jessica Gutknecht; N. R. Chiariello; Audrey Niboyet; Audrey Niboyet; Christopher B. Field; Bruce A. Hungate; Jizhong Zhou; Jizhong Zhou; Jizhong Zhou; Yunfeng Yang; Qiaoshu Zheng; Mengting Yuan; Sihang Yang; Xavier Le Roux; Kathryn M. Docherty;doi: 10.1111/gcb.14852
pmid: 31562826
AbstractFire is a crucial event regulating the structure and functioning of many ecosystems. Yet few studies have focused on how fire affects taxonomic and functional diversities of soil microbial communities, along with changes in plant communities and soil carbon (C) and nitrogen (N) dynamics. Here, we analyze these effects in a grassland ecosystem 9 months after an experimental fire at the Jasper Ridge Global Change Experiment site in California, USA. Fire altered soil microbial communities considerably, with community assembly process analysis showing that environmental selection pressure was higher in burned sites. However, a small subset of highly connected taxa was able to withstand the disturbance. In addition, fire decreased the relative abundances of most functional genes associated with C degradation and N cycling, implicating a slowdown of microbial processes linked to soil C and N dynamics. In contrast, fire stimulated above‐ and belowground plant growth, likely enhancing plant–microbe competition for soil inorganic N, which was reduced by a factor of about 2. To synthesize those findings, we performed structural equation modeling, which showed that plants but not microbial communities were responsible for significantly higher soil respiration rates in burned sites. Together, our results demonstrate that fire ‘reboots’ the grassland ecosystem by differentially regulating plant and soil microbial communities, leading to significant changes in soil C and N dynamics.
Global Change Biolog... arrow_drop_down Global Change BiologyArticle . 2019 . Peer-reviewedLicense: Wiley Online Library User AgreementData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1111/gcb.14852&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen hybrid 49 citations 49 popularity Top 1% influence Average impulse Top 10% Powered by BIP!
more_vert Global Change Biolog... arrow_drop_down Global Change BiologyArticle . 2019 . Peer-reviewedLicense: Wiley Online Library User AgreementData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1111/gcb.14852&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Journal 2017 Russian Federation, United StatesPublisher:Wiley Nianpeng He; Yuan Liu; Jizhong Zhou; Jizhong Zhou; Jizhong Zhou; Jing Tian; Qun Gao; Qun Gao; Guirui Yu; Evgenia Blagodatskaya; Yakov Kuzyakov; Lauren Hale; Shuli Niu;Abstract Bacteria are one of the most abundant and diverse groups of micro‐organisms and mediate many critical terrestrial ecosystem processes. Despite the crucial ecological role of bacteria, our understanding of their large‐scale biogeography patterns across forests, and the processes that determine these patterns lags significantly behind that of macroorganisms. Here, we evaluated the geographic distributions of bacterial diversity and their driving factors across nine latitudinal forests along a 3,700‐km north–south transect in eastern China, using high‐throughput 16S rRNA gene sequencing. Four of 32 phyla detected were dominant: Acidobacteria, Actinobacteria, Alphaproteobacteria and Chloroflexi (relative abundance > 5%). Significant increases in bacterial richness and phylogenetic diversity were observed for temperate forests compared with subtropical or tropical forests. The soil organic matter (SOM) mineralisation rate (SOMmin, an index of SOM availability) explained the largest significant variations in bacterial richness. Variation partition analysis revealed that the bacterial community structure was closely correlated with environmental variables and geographic distance, which together explained 80.5% of community variation. Among all environmental factors, climatic features (MAT and MAP) were the best predictors of the bacterial community structure, whereas soil pH and SOMmin emerged as the most important edaphic drivers of the bacterial community structure. Plant functional traits (community weighted means of litter N content) and diversity resulted in weak but significant correlations with the bacterial community structure. Our findings provide new evidence of bacterial biogeography patterns from tropical to cold temperate forests. Additionally, the results indicated a close linkage among soil bacterial diversity, climate and SOM decomposition, which is critical for predicting continental‐scale responses under future climate change scenarios and promoting sustainable forest ecosystem services. A plain language summary is available for this article.
Functional Ecology arrow_drop_down Functional EcologyArticle . 2017 . Peer-reviewedLicense: Wiley Online Library User AgreementData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1111/1365-2435.12952&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen bronze 121 citations 121 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!
more_vert Functional Ecology arrow_drop_down Functional EcologyArticle . 2017 . Peer-reviewedLicense: Wiley Online Library User AgreementData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1111/1365-2435.12952&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2023Publisher:Wiley Mengmeng Wang; Xin Sun; Baichuan Cao; Nona R. Chiariello; Kathryn M. Docherty; Christopher B. Field; Qun Gao; Jessica L. M. Gutknecht; Xue Guo; Genhe He; Bruce A. Hungate; Jiesi Lei; Audrey Niboyet; Xavier Le Roux; Zhou Shi; Wensheng Shu; Mengting Yuan; Jizhong Zhou; Yunfeng Yang;doi: 10.1111/gcb.16811
pmid: 37317051
AbstractGlobal climate models predict that the frequency and intensity of precipitation events will increase in many regions across the world. However, the biosphere‐climate feedback to elevated precipitation (eP) remains elusive. Here, we report a study on one of the longest field experiments assessing the effects of eP, alone or in combination with other climate change drivers such as elevated CO2 (eCO2), warming and nitrogen deposition. Soil total carbon (C) decreased after a decade of eP treatment, while plant root production decreased after 2 years. To explain this asynchrony, we found that the relative abundances of fungal genes associated with chitin and protein degradation increased and were positively correlated with bacteriophage genes, suggesting a potential viral shunt in C degradation. In addition, eP increased the relative abundances of microbial stress tolerance genes, which are essential for coping with environmental stressors. Microbial responses to eP were phylogenetically conserved. The effects of eP on soil total C, root production, and microbes were interactively affected by eCO2. Collectively, we demonstrate that long‐term eP induces soil C loss, owing to changes in microbial community composition, functional traits, root production, and soil moisture. Our study unveils an important, previously unknown biosphere‐climate feedback in Mediterranean‐type water‐limited ecosystems, namely how eP induces soil C loss via microbe‐plant–soil interplay.
Global Change Biolog... arrow_drop_down Global Change BiologyArticle . 2023 . Peer-reviewedLicense: Wiley Online Library User AgreementData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1111/gcb.16811&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen bronze 8 citations 8 popularity Top 10% influence Average impulse Top 10% Powered by BIP!
more_vert Global Change Biolog... arrow_drop_down Global Change BiologyArticle . 2023 . Peer-reviewedLicense: Wiley Online Library User AgreementData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1111/gcb.16811&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Journal 2010 United StatesPublisher:American Society for Microbiology Safiyh Taghavi; Housna Mouttaki; Liyou Wu; Alla Lapidus; Jonathan R. Mielenz; Elizabeth Saunders; Joy D. Van Nostrand; Nikos C. Kyrpides; Matthew W. Fields; Bradley S. Stevenson; Bernard Henrissat; Sam Pitluck; Michael E. Himmel; Raymond L. Huhnke; Zhili He; Cliff Han; Tijana Glavina del Rio; Michael J. McInerney; Qiang He; Jizhong Zhou; Lynne Goodwin; Gengxin Zhang; Natalia Mikhailova; Aijie Wang; Hope Tice; Christopher W. Schadt; Yunfeng Yang; Daniel van der Lelie; Yong-Jin Lee; Defeng Xing; Shi You Ding; Susan Lucas; Ralph S. Tanner; Miriam Land; Loren Hauser; Thomas Brettin; Thomas Brettin; Christopher L. Hemme; Adam P. Arkin; Hailiang Dong; Edward M. Rubin; Nanqi Ren; Juergen Wiegel; Alex Copeland; John C. Detter; Paul A. Lawson; Lee R. Lynd;ABSTRACT Modern methods to develop microbe-based biomass conversion processes require a system-level understanding of the microbes involved. Clostridium species have long been recognized as ideal candidates for processes involving biomass conversion and production of various biofuels and other industrial products. To expand the knowledge base for clostridial species relevant to current biofuel production efforts, we have sequenced the genomes of 20 species spanning multiple genera. The majority of species sequenced fall within the class III cellulosome-encoding Clostridium and the class V saccharolytic Thermoanaerobacteraceae . Species were chosen based on representation in the experimental literature as model organisms, ability to degrade cellulosic biomass either by free enzymes or by cellulosomes, ability to rapidly ferment hexose and pentose sugars to ethanol, and ability to ferment synthesis gas to ethanol. The sequenced strains significantly increase the number of noncommensal/nonpathogenic clostridial species and provide a key foundation for future studies of biomass conversion, cellulosome composition, and clostridial systems biology.
Journal of Bacteriol... arrow_drop_down Journal of BacteriologyArticle . 2010 . Peer-reviewedLicense: ASM Journals Non-Commercial TDMData sources: CrossrefUniversity of Oklahoma/Oklahoma State University: SHAREOK RepositoryArticle . 2015Data sources: Bielefeld Academic Search Engine (BASE)add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1128/jb.01064-10&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen bronze 76 citations 76 popularity Top 10% influence Top 10% impulse Top 10% Powered by BIP!
more_vert Journal of Bacteriol... arrow_drop_down Journal of BacteriologyArticle . 2010 . Peer-reviewedLicense: ASM Journals Non-Commercial TDMData sources: CrossrefUniversity of Oklahoma/Oklahoma State University: SHAREOK RepositoryArticle . 2015Data sources: Bielefeld Academic Search Engine (BASE)add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://beta.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1128/jb.01064-10&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu