scholarly journals Stable Soil Microbial Functional Structure Responding to Biodiversity Loss Based on Metagenomic Evidences

2021 ◽  
Vol 12 ◽  
Author(s):  
Huaihai Chen ◽  
Kayan Ma ◽  
Yu Huang ◽  
Zhiyuan Yao ◽  
Chengjin Chu
Keyword(s):  
Large Scale ◽  
Global Climate ◽  
Biodiversity Loss ◽  
Functional Structure ◽  
Metagenomic Data ◽  
Ecosystem Functions ◽  
Soil Microbial ◽  
Microbial Species ◽  
The Stability ◽  
And Function

Anthropogenic disturbances and global climate change are causing large-scale biodiversity loss and threatening ecosystem functions. However, due to the lack of knowledge on microbial species loss, our understanding on how functional profiles of soil microbes respond to diversity decline is still limited. Here, we evaluated the biotic homogenization of global soil metagenomic data to examine whether microbial functional structure is resilient to significant diversity reduction. Our results showed that although biodiversity loss caused a decrease in taxonomic species by 72%, the changes in the relative abundance of diverse functional categories were limited. The stability of functional structures associated with microbial species richness decline in terrestrial systems suggests a decoupling of taxonomy and function. The changes in functional profile with biodiversity loss were function-specific, with broad-scale metabolism functions decreasing and typical nutrient-cycling functions increasing. Our results imply high levels of microbial physiological versatility in the face of significant biodiversity decline, which, however, does not necessarily mean that a loss in total functional abundance, such as microbial activity, can be overlooked in the background of unprecedented species extinction.

scholarly journals Energetic dependencies dictate folding mechanism in a complex protein

2019 ◽  
Vol 116 (51) ◽  
pp. 25641-25648 ◽  
Author(s):  
Kaixian Liu ◽  
Xiuqi Chen ◽  
Christian M. Kaiser
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Large Scale ◽  
Elongation Factor ◽  
Multidomain Protein ◽  
Domain Interactions ◽  
The Stability ◽  
Domain Iii ◽  
And Function ◽  
Terminal Domains

Large proteins with multiple domains are thought to fold cotranslationally to minimize interdomain misfolding. Once folded, domains interact with each other through the formation of extensive interfaces that are important for protein stability and function. However, multidomain protein folding and the energetics of domain interactions remain poorly understood. In elongation factor G (EF-G), a highly conserved protein composed of 5 domains, the 2 N-terminal domains form a stably structured unit cotranslationally. Using single-molecule optical tweezers, we have defined the steps leading to fully folded EF-G. We find that the central domain III of EF-G is highly dynamic and does not fold upon emerging from the ribosome. Surprisingly, a large interface with the N-terminal domains does not contribute to the stability of domain III. Instead, it requires interactions with its folded C-terminal neighbors to be stably structured. Because of the directionality of protein synthesis, this energetic dependency of domain III on its C-terminal neighbors disrupts cotranslational folding and imposes a posttranslational mechanism on the folding of the C-terminal part of EF-G. As a consequence, unfolded domains accumulate during synthesis, leading to the extensive population of misfolded species that interfere with productive folding. Domain III flexibility enables large-scale conformational transitions that are part of the EF-G functional cycle during ribosome translocation. Our results suggest that energetic tuning of domain stabilities, which is likely crucial for EF-G function, complicates the folding of this large multidomain protein.

scholarly journals From single nuclei to whole genome assemblies

2019 ◽  
Author(s):  
Merce Montoliu-Nerin ◽  
Marisol Sánchez-García ◽  
Claudia Bergin ◽  
Manfred Grabherr ◽  
Barbara Ellis ◽  
...  
Keyword(s):  
Single Cell ◽  
Large Scale ◽  
Genomic Data ◽  
Life Cycles ◽  
Genomic Research ◽  
Metagenomic Data ◽  
Model Organisms ◽  
Genomic Study ◽  
And Function ◽  
Genome Assemblies

SummaryA large proportion of Earth's biodiversity constitutes organisms that cannot be cultured, have cryptic life-cycles and/or live submerged within their substrates1–4. Genomic data are key to unravel both their identity and function5. The development of metagenomic methods6,7 and the advent of single cell sequencing8–10 have revolutionized the study of life and function of cryptic organisms by upending the need for large and pure biological material, and allowing generation of genomic data from complex or limited environmental samples. Genome assemblies from metagenomic data have so far been restricted to organisms with small genomes, such as bacteria11, archaea12 and certain eukaryotes13. On the other hand, single cell technologies have allowed the targeting of unicellular organisms, attaining a better resolution than metagenomics8,9,14–16, moreover, it has allowed the genomic study of cells from complex organisms one cell at a time17,18. However, single cell genomics are not easily applied to multicellular organisms formed by consortia of diverse taxa, and the generation of specific workflows for sequencing and data analysis is needed to expand genomic research to the entire tree of life, including sponges19, lichens3,20, intracellular parasites21,22, and plant endophytes23,24. Among the most important plant endophytes are the obligate mutualistic symbionts, arbuscular mycorrhizal (AM) fungi, that pose an additional challenge with their multinucleate coenocytic mycelia25. Here, the development of a novel single nuclei sequencing and assembly workflow is reported. This workflow allows, for the first time, the generation of reference genome assemblies from large scale, unbiased sorted, and sequenced AM fungal nuclei circumventing tedious, and often impossible, culturing efforts. This method opens infinite possibilities for studies of evolution and adaptation in these important plant symbionts and demonstrates that reference genomes can be generated from complex non-model organisms by isolating only a handful of their nuclei.

scholarly journals Vulnerability and resistance in the spatial heterogeneity of soil microbial communities under resource additions

2020 ◽  
Vol 117 (13) ◽  
pp. 7263-7270 ◽  
Author(s):  
Kelly Gravuer ◽  
Anu Eskelinen ◽  
Joy B. Winbourne ◽  
Susan P. Harrison
Keyword(s):  
Spatial Variability ◽  
Spatial Heterogeneity ◽  
Soil Microbial Communities ◽  
Archaeal Community ◽  
Ecosystem Functions ◽  
Water Addition ◽  
Microbial Composition ◽  
Soil Microbial ◽  
The Face ◽  
And Function

Spatial heterogeneity in composition and function enables ecosystems to supply diverse services. For soil microbes and the ecosystem functions they catalyze, whether such heterogeneity can be maintained in the face of altered resource inputs is uncertain. In a 50-ha northern California grassland with a mosaic of plant communities generated by different soil types, we tested how spatial variability in microbial composition and function changed in response to nutrient and water addition. Fungal composition lost some of its spatial variability in response to nutrient addition, driven by decreases in mutualistic fungi and increases in antagonistic fungi that were strongest on the least fertile soils, where mutualists were initially most frequent and antagonists initially least frequent. Bacterial and archaeal community composition showed little change in their spatial variability with resource addition. Microbial functions related to nitrogen cycling showed increased spatial variability under nutrient, and sometimes water, additions, driven in part by accelerated nitrification on the initially more-fertile soils. Under anthropogenic changes such as eutrophication and altered rainfall, these findings illustrate the potential for significant changes in ecosystem-level spatial heterogeneity of microbial functions and communities.

Pengembangan Nontransgenik F1 dan Bc1f1 Padi Ciherang Toleran Genangan secara Site-Directed Crossing

2014 ◽  
Vol 1 (3) ◽  
pp. 136-145
Author(s):  
Djarot Sasongko Hami Seno ◽  
Satya Nugroho ◽  
Tri Joko Santoso ◽  
Joel Rivandi Sinaga ◽  
Euis Marlina ◽  
...  
Keyword(s):  
Large Scale ◽  
Agronomic Traits ◽  
Global Climate ◽  
Rice Variety ◽  
Submergence Tolerance ◽  
Rice Varieties ◽  
Global Climate Changes ◽  
Tolerance Gene ◽  
The Stability ◽  
Large Scale Cultivation

The development of submergence tolerant rice varieties is urgently required to maintain the stability of future food production, to anticipate the unpredictable global climate changes. Due to in-economical agronomic traits of native submergence tolerant varieties for large scale cultivation, submergence tolerance gene (sub1) must be introduced into popular high-yielding rice variety, such as Ciherang. To develop new submergence tolerant variety with good agronomic traits as those of Ciherang, in this research, submergence tolerance gene (sub1) was introduced into Ciherang variety. To avoid strict GMO regulation, gene introduction was carried out through site-directed crossing. Donor sub1 was crossed with Ciherang host. The selected F1 progenies were further backcrossed to Ciherang 4 x to obtain BC5F1 progeny having ~98% agronomic traits of those of Ciherang. In every cross/backcross generation, submergence test was performed, followed by sub1 marker-assisted PCR. F1 and BC1F1 submergence-tolerant Ciherang were successfully constructed. Co-dominant RM464A marker was not able to discriminate between host, donor, and progenies (F1 and BC1). Co-dominant RM219 maker showed slightly different size between donor and host amplicon, but it was difficult to see their heterozygous progenies. Both C173 and AEX1 dominant markers were able to show sub1 introgression from donor to host. PCR results confirmed that progenies-submergence tolerance was due to sub1 introgression, not escape mechanisms. AEX1 was chosen for subsequent experiments. Backcross until BC5 is in progress, to obtain maximum host retention for engineering new submergence tolerant varieties with good agronomic traits as those of Ciherang.

scholarly journals Soil Microbial Community Responses to a Decade of Warming as Revealed by Comparative Metagenomics

2013 ◽  
Vol 80 (5) ◽  
pp. 1777-1786 ◽  
Author(s):  
Chengwei Luo ◽  
Luis M. Rodriguez-R ◽  
Eric R. Johnston ◽  
Liyou Wu ◽  
Lei Cheng ◽  
...  
Keyword(s):  
Climate Change ◽  
Microbial Communities ◽  
Molecular Mechanisms ◽  
Cellulose Degradation ◽  
Global Climate ◽  
Soil Microbial Communities ◽  
Predictive Ability ◽  
Metagenomic Data ◽  
Data Sets ◽  
Soil Microbial

ABSTRACTSoil microbial communities are extremely complex, being composed of thousands of low-abundance species (<0.1% of total). How such complex communities respond to natural or human-induced fluctuations, including major perturbations such as global climate change, remains poorly understood, severely limiting our predictive ability for soil ecosystem functioning and resilience. In this study, we compared 12 whole-community shotgun metagenomic data sets from a grassland soil in the Midwestern United States, half representing soil that had undergone infrared warming by 2°C for 10 years, which simulated the effects of climate change, and the other half representing the adjacent soil that received no warming and thus, served as controls. Our analyses revealed that the heated communities showed significant shifts in composition and predicted metabolism, and these shifts were community wide as opposed to being attributable to a few taxa. Key metabolic pathways related to carbon turnover, such as cellulose degradation (∼13%) and CO2production (∼10%), and to nitrogen cycling, including denitrification (∼12%), were enriched under warming, which was consistent with independent physicochemical measurements. These community shifts were interlinked, in part, with higher primary productivity of the aboveground plant communities stimulated by warming, revealing that most of the additional, plant-derived soil carbon was likely respired by microbial activity. Warming also enriched for a higher abundance of sporulation genes and genomes with higher G+C content. Collectively, our results indicate that microbial communities of temperate grassland soils play important roles in mediating feedback responses to climate change and advance the understanding of the molecular mechanisms of community adaptation to environmental perturbations.

scholarly journals Crosstalk Between SUMO and Ubiquitin-Like Proteins: Implication for Antiviral Defense

2021 ◽  
Vol 9 ◽  
Author(s):  
Mounira K. Chelbi-Alix ◽  
Pierre Thibault
Keyword(s):  
Large Scale ◽  
Ring Finger ◽  
Dependent Manner ◽  
Antiviral Defense ◽  
Restriction Factors ◽  
Protein Conjugates ◽  
Antiviral Activities ◽  
Quantitative Changes ◽  
The Stability ◽  
And Function

Interferon (IFN) is a crucial first line of defense against viral infection. This cytokine induces the expression of several IFN-Stimulated Genes (ISGs), some of which act as restriction factors. Upon IFN stimulation, cells also express ISG15 and SUMO, two key ubiquitin-like (Ubl) modifiers that play important roles in the antiviral response. IFN itself increases the global cellular SUMOylation in a PML-dependent manner. Mass spectrometry-based proteomics enables the large-scale identification of Ubl protein conjugates to determine the sites of modification and the quantitative changes in protein abundance. Importantly, a key difference amongst SUMO paralogs is the ability of SUMO2/3 to form poly-SUMO chains that recruit SUMO ubiquitin ligases such RING finger protein RNF4 and RNF111, thus resulting in the proteasomal degradation of conjugated substrates. Crosstalk between poly-SUMOylation and ISG15 has been reported recently, where increased poly-SUMOylation in response to IFN enhances IFN-induced ISGylation, stabilizes several ISG products in a TRIM25-dependent fashion, and results in enhanced IFN-induced antiviral activities. This contribution will highlight the relevance of the global SUMO proteome and the crosstalk between SUMO, ubiquitin and ISG15 in controlling both the stability and function of specific restriction factors that mediate IFN antiviral defense.

scholarly journals Biotic homogenization can decrease landscape-scale forest multifunctionality

2016 ◽  
Vol 113 (13) ◽  
pp. 3557-3562 ◽  
Author(s):  
Fons van der Plas ◽  
Pete Manning ◽  
Santiago Soliveres ◽  
Eric Allan ◽  
Michael Scherer-Lorenzen ◽  
...  
Keyword(s):  
Large Scale ◽  
Biodiversity Loss ◽  
Landscape Scale ◽  
Biotic Homogenization ◽  
Ecosystem Functions ◽  
Negative Consequences ◽  
Β Diversity ◽  
Spatial Turnover ◽  
Α Diversity ◽  
Ecosystem Multifunctionality

Many experiments have shown that local biodiversity loss impairs the ability of ecosystems to maintain multiple ecosystem functions at high levels (multifunctionality). In contrast, the role of biodiversity in driving ecosystem multifunctionality at landscape scales remains unresolved. We used a comprehensive pan-European dataset, including 16 ecosystem functions measured in 209 forest plots across six European countries, and performed simulations to investigate how local plot-scale richness of tree species (α-diversity) and their turnover between plots (β-diversity) are related to landscape-scale multifunctionality. After accounting for variation in environmental conditions, we found that relationships between α-diversity and landscape-scale multifunctionality varied from positive to negative depending on the multifunctionality metric used. In contrast, when significant, relationships between β-diversity and landscape-scale multifunctionality were always positive, because a high spatial turnover in species composition was closely related to a high spatial turnover in functions that were supported at high levels. Our findings have major implications for forest management and indicate that biotic homogenization can have previously unrecognized and negative consequences for large-scale ecosystem multifunctionality.

scholarly journals MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun meta-genomic data

2017 ◽  
Author(s):  
Florian Plaza Oñate ◽  
Emmanuelle Le Chatelier ◽  
Mathieu Almeida ◽  
Ales-sandra C. L. Cervino ◽  
Franck Gauthier ◽  
...  
Keyword(s):  
Large Scale ◽  
De Novo ◽  
Software Tool ◽  
Supplementary Information ◽  
Metagenomic Data ◽  
Gene Repertoire ◽  
Human Gut ◽  
Taxonomic Profiling ◽  
Microbial Species ◽  
Accessory Genes

AbstractMotivationAnalysis toolkits for shotgun metagenomic data achieve strain-level characterization of complex microbial communities by capturing intra-species gene content variation. Yet, these tools are hampered by the extent of reference genomes that are far from covering all microbial variability, as many species are still not sequenced or have only few strains available. Binning co-abundant genes obtained from de novo assembly is a powerful reference-free technique to discover and reconstitute gene repertoire of microbial species. While current methods accurately identify species core parts, they miss many accessory genes or split them into small gene groups that remain unassociated to core clusters.ResultsWe introduce MSPminer, a computationally efficient software tool that reconstitutes Metagenomic Species Pan-genomes (MSPs) by binning co-abundant genes across metagenomic samples. MSPminer relies on a new robust measure of proportionality coupled with an empirical classifier to group and distinguish not only species core genes but accessory genes also. Applied to a large scale metagenomic dataset, MSPminer successfully delineates in a few hours the gene repertoires of 1 661 microbial species with similar specificity and higher sensitivity than existing tools. The taxonomic annotation of MSPs reveals microorganisms hitherto unknown and brings coherence in the nomenclature of the species of the human gut microbiota. The provided MSPs can be readily used for taxonomic profiling and biomarkers discovery in human gut metagenomic samples. In addition, MSPminer can be applied on gene count tables from other ecosystems to perform similar analyses.AvailabilityThe binary is freely available for non-commercial users at enterome.fr/site/downloads/ Contact: [email protected] informationAvailable in the file named Supplementary Information.pdf

scholarly journals Effects of global warming on plateau plants

2021 ◽  
pp. 963-968
Author(s):  
Dan Wu ◽  
Hui Kong
Keyword(s):  
Large Scale ◽  
Global Climate ◽  
Future Research ◽  
Response Patterns ◽  
Physiological Level ◽  
Survival And Development ◽  
Response Modes ◽  
Different Response ◽  
And Function ◽  
Change Response

Biological and ecological environment in the plateau climate warming, abiotic environmental factors to different degrees of change were summed up from the macroscopic level to microcosmic individual physiological level of global climate change response model. The study summarized the research achievements at home and abroad, pointed out the plant phenology, photosynthesis, nutrient structure and presents different response patterns. These different response modes, from micro to macro, will eventually lead to changes in the structure and function of the Plateau ecosystem. This will threaten the survival and development of the Plateau plants on a large scale. Finally, the future research emphases in this field would be prospected. Bangladesh J. Bot. 50(3): 963-968, 2021 (September) Special

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