scholarly journals Community RNA-Seq: multi-kingdom responses to living versus decaying roots in soil

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Erin E. Nuccio ◽  
Nhu H. Nguyen ◽  
Ulisses Nunes da Rocha ◽  
Xavier Mayali ◽  
Jeremy Bougoure ◽  
...  
Keyword(s):  
Root Exudates ◽  
Community Dynamics ◽  
Primary Source ◽  
Community Analysis ◽  
Bulk Soil ◽  
Rna Seq ◽  
Microbial Life ◽  
Complex Interactions ◽  
Elemental Cycling ◽  
Root Litter

AbstractRoots are a primary source of organic carbon input in most soils. The consumption of living and detrital root inputs involves multi-trophic processes and multiple kingdoms of microbial life, but typical microbial ecology studies focus on only one or two major lineages. We used Illumina shotgun RNA sequencing to conduct PCR-independent SSU rRNA community analysis (“community RNA-Seq”) and simultaneously assess the bacteria, archaea, fungi, and microfauna surrounding both living and decomposing roots of the annual grass, Avena fatua. Plants were grown in 13CO2-labeled microcosms amended with 15N-root litter to identify the preferences of rhizosphere organisms for root exudates (13C) versus decaying root biomass (15N) using NanoSIMS microarray imaging (Chip-SIP). When litter was available, rhizosphere and bulk soil had significantly more Amoebozoa, which are potentially important yet often overlooked top-down drivers of detritusphere community dynamics and nutrient cycling. Bulk soil containing litter was depleted in Actinobacteria but had significantly more Bacteroidetes and Proteobacteria. While Actinobacteria were abundant in the rhizosphere, Chip-SIP showed Actinobacteria preferentially incorporated litter relative to root exudates, indicating this group’s more prominent role in detritus elemental cycling in the rhizosphere. Our results emphasize that decomposition is a multi-trophic process involving complex interactions, and our methodology can be used to track the trajectory of carbon through multi-kingdom soil food webs.

scholarly journals Community RNA-Seq: Multi-kingdom responses to living versus decaying root inputs in soil

2021 ◽  
Author(s):  
Erin E. Nuccio ◽  
Nhu H. Nguyen ◽  
Ulisses Nunes da Rocha ◽  
Xavier Mayali ◽  
Jeremy Bougoure ◽  
...  
Keyword(s):  
Community Dynamics ◽  
Primary Source ◽  
Community Analysis ◽  
Bulk Soil ◽  
Rna Seq ◽  
Soil Food Web ◽  
Microbial Life ◽  
Substrate Preferences ◽  
Elemental Cycling ◽  
Root Litter

ABSTRACTRoots are the primary source of organic carbon inputs to most soils. Decomposition is a multi-trophic process involving multiple kingdoms of microbial life, but typically microbial ecology studies focus on one or two major lineages in isolation. We used Illumina shotgun RNA sequencing to conduct PCR-independent SSU rRNA community analysis (“community RNA-Seq”) to simultaneously study the bacteria, archaea, fungi, and microfauna surrounding both living and decomposing roots of the annual grass, Avena fatua. Plants were grown in 13CO2-labeled microcosms amended with 15N-root litter. We identified rhizosphere substrate preferences for 13C-exudates versus 15N-litter using NanoSIMS microarray imaging (Chip-SIP). When litter was available, rhizosphere and bulk soil had significantly more Amoebozoa, which are potentially important yet often overlooked top-down drivers of detritusphere community dynamics and nutrient cycling. Bulk soil containing litter was depleted in Actinobacteria but had significantly more Bacteroidetes and Proteobacteria. While Actinobacteria were abundant in the rhizosphere, Chip-SIP showed Actinobacteria preferentially incorporated litter relative to root exudates, indicating this group’s more prominent role in detritus elemental cycling in the rhizosphere. Our results emphasize that decomposition is a multi-trophic process involving cross-kingdom interactions, and the trajectory of carbon through this soil food web likely impacts the fate of carbon in soil.

Warming increases soil carbon input in a Sibiraea angustata-dominated alpine shrub ecosystem

2021 ◽  
Author(s):  
Mei Liu ◽  
Jia-Hao Wen ◽  
Ya-Mei Chen ◽  
Wen-Juan Xu ◽  
Qiong Wang ◽  
...  
Keyword(s):  
Tibetan Plateau ◽  
Root Exudates ◽  
Climate Warming ◽  
Root Exudate ◽  
Soil Organic C ◽  
Organic C ◽  
Root Litter ◽  
C Stocks ◽  
Alpine Shrub ◽  
Key Drivers

Abstract Aims Plant-derived carbon (C) inputs via foliar litter, root litter and root exudates are key drivers of soil organic C stocks. However, the responses of these three input pathways to climate warming have rarely been studied in alpine shrublands. Methods By employing a three-year warming experiment (increased by1.3 ℃), we investigated the effects of warming on the relative C contributions from foliar litter, root litter and root exudates from Sibiraea angustata, a dominant shrub species in an alpine shrubland on the eastern Qinghai-Tibetan Plateau. Important Findings The soil organic C inputs from foliar litter, root litter and root exudates were 77.45, 90.58 and 26.94 g C m -2, respectively. Warming only slightly increased the soil organic C inputs from foliar litter and root litter by 8.04 and 11.13 g C m -2, but significantly increased the root exudate C input by 15.40 g C m -2. Warming significantly increased the relative C contributions of root exudates to total C inputs by 4.6% but slightly decreased those of foliar litter and root litter by 2.5% and 2.1%, respectively. Our results highlight that climate warming may stimulate plant-derived C inputs into soils mainly through root exudates rather than litter in alpine shrublands on the Qinghai-Tibetan Plateau.

scholarly journals Complex interactions in legume/cereal intercropping system: role of root exudates in root-to-root communication

2017 ◽  
Author(s):  
Yinshan Jiao ◽  
Entao Wang ◽  
Wenfeng Chen ◽  
Donald L. Smith
Keyword(s):  
Nitrogen Fixation ◽  
Root Exudates ◽  
Faba Bean ◽  
The Novel ◽  
Practical Application ◽  
Corn Root ◽  
Complex Interactions ◽  
Root Interactions ◽  
Ecological Principles

Dear Editor,Legume/cereal intercropping systems have been regarded as the practical application of basic ecological principles such as diversity, competition and facilitation. In a recent PNAS paper, Li et al. (1) describe the novel finding that maize exudates promote faba bean nodulation and nitrogen fixation by upregulating genes involved in (iso)flavonoids synthesis (chalcone–flavanone isomerase) within faba bean, resulting in production of more genistein, a legume-to-rhizobia signal during establishment of the faba bean N2–fixing symbiosis. Although we salute the authors’ methodological efforts, there is another mechanism that could be responsible for the effect of corn root exudates on faba been nitrogen fixation observed in this article (1). The authors may misunderstand their data and the signalling role of maize exudates, thus got a defective model for the root interactions between faba bean and maize.

scholarly journals Viruses of Polar Aquatic Environments

Viruses ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 189 ◽  
Author(s):  
Sheree Yau ◽  
Mansha Seth-Pasricha
Keyword(s):  
Community Dynamics ◽  
Spatial Scales ◽  
Extreme Environments ◽  
Cold Climate ◽  
Polar Regions ◽  
Microbial Life ◽  
The North ◽  
Cellular Life ◽  
Antarctic Continent ◽  
Cycling Of Nutrients

The poles constitute 14% of the Earth’s biosphere: The aquatic Arctic surrounded by land in the north, and the frozen Antarctic continent surrounded by the Southern Ocean. In spite of an extremely cold climate in addition to varied topographies, the polar aquatic regions are teeming with microbial life. Even in sub-glacial regions, cellular life has adapted to these extreme environments where perhaps there are traces of early microbes on Earth. As grazing by macrofauna is limited in most of these polar regions, viruses are being recognized for their role as important agents of mortality, thereby influencing the biogeochemical cycling of nutrients that, in turn, impact community dynamics at seasonal and spatial scales. Here, we review the viral diversity in aquatic polar regions that has been discovered in the last decade, most of which has been revealed by advances in genomics-enabled technologies, and we reflect on the vast extent of the still-to-be explored polar microbial diversity and its “enigmatic virosphere”.

scholarly journals Corynebacterium Comparative Genomics Reveals a Role for Cobamide Sharing in the Skin Microbiome

2020 ◽  
Author(s):  
Mary Hannah Swaney ◽  
Lindsay R Kalan
Keyword(s):  
Comparative Genomics ◽  
Microbial Communities ◽  
Community Dynamics ◽  
De Novo ◽  
Skin Barrier ◽  
Skin Microbiome ◽  
Bacterial Phyla ◽  
Host Interactions ◽  
Complex Interactions ◽  
Associated Species

ABSTRACTThe human skin microbiome is a key player in human health, with diverse functions ranging from defense against pathogens to education of the immune system. Recent studies have begun unraveling the complex interactions within skin microbial communities, shedding light on the invaluable role that skin microorganisms have in maintaining a healthy skin barrier. While the Corynebacterium genus is a dominant taxon of the skin microbiome, relatively little is known how skin-associated Corynebacteria contribute to microbe-microbe and microbe-host interactions on the skin. Here, we performed a comparative genomics analysis of 71 Corynebacterium species from diverse ecosystems, which revealed functional differences between host- and environment-associated species. In particular, host-associated species were enriched for de novo biosynthesis of cobamides, which are a class of cofactor essential for metabolism in organisms across the tree of life but are produced by a limited number of prokaryotes. Because cobamides have been hypothesized to mediate community dynamics within microbial communities, we analyzed skin metagenomes for Corynebacterium cobamide producers, which revealed a positive correlation between cobamide producer abundance and microbiome diversity, a trait associated with skin health. We also provide the first metagenome-based assessment of cobamide biosynthesis and utilization in the skin microbiome, showing that both dominant and low abundant skin taxa encode for the de novo biosynthesis pathway and that cobamide-dependent enzymes are encoded by phylogenetically diverse taxa across the major bacterial phyla on the skin. Taken together, our results support a role for cobamide sharing within skin microbial communities, which we hypothesize mediates community dynamics.

scholarly journals Approaching mercury distribution in burial environment using PLS-R modelling

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Noemi Álvarez-Fernández ◽  
Antonio Martínez Cortizas ◽  
Zaira García-López ◽  
Olalla López-Costas
Keyword(s):  
Soft Tissues ◽  
Primary Source ◽  
Secondary Source ◽  
Sources Of Information ◽  
Mercury Distribution ◽  
The Past ◽  
Complex Interactions ◽  
Target Organs ◽  
History Of ◽  
The One

AbstractMercury environmental cycle and toxicology have been widely researched. Given the long history of mercury pollution, researching mercury trends in the past can help to understand its behaviour in the present. Archaeological skeletons have been found to be useful sources of information regarding mercury loads in the past. In our study we applied a soil multi-sampling approach in two burials dated to the 5th to 6th centuries AD. PLRS modelling was used to elucidate the factors controlling mercury distribution. The model explains 72% of mercury variance and suggests that mercury accumulation in the burial soils is the result of complex interactions. The decomposition of the bodies not only was the primary source of mercury to the soil but also responsible for the pedogenetic transformation of the sediments and the formation of soil components with the ability to retain mercury. The amount of soft tissues and bone mass also resulted in differences between burials, indicating that the skeletons were a primary/secondary source of mercury to the soil (i.e. temporary sink). Within burial variability seems to depend on the proximity of the soil to the thoracic area, where the main mercury target organs were located. We also conclude that, in coarse textured soils, as the ones studied in this investigation, the finer fraction (i.e. silt + clay) should be analysed, as it is the most reactive and the one with the higher potential to provide information on metal cycling and incipient soil processes. Finally, our study stresses the need to characterise the burial soil environment in order to fully understand the role of the interactions between soil and skeleton in mercury cycling in burial contexts.

scholarly journals Application of Functional Genomics for Bovine Respiratory Disease Diagnostics

2015 ◽  
Vol 9s2 ◽  
pp. BBI.S30525 ◽  
Author(s):  
Aswathy N. Rai ◽  
William B. Epperson ◽  
Bindu Nanduri
Keyword(s):  
Functional Genomics ◽  
Respiratory Disease ◽  
High Throughput ◽  
Molecular Mechanisms ◽  
Bovine Respiratory Disease ◽  
Rna Seq ◽  
Complex Interactions ◽  
Disease Diagnostics ◽  
Genome Scale ◽  
Important Disease

Bovine respiratory disease (BRD) is the most common economically important disease affecting cattle. For developing accurate diagnostics that can predict disease susceptibility/resistance and stratification, it is necessary to identify the molecular mechanisms that underlie BRD. To study the complex interactions among the bovine host and the multitude of viral and bacterial pathogens, as well as the environmental factors associated with BRD etiology, genome-scale high-throughput functional genomics methods such as microarrays, RNA-seq, and proteomics are helpful. In this review, we summarize the progress made in our understanding of BRD using functional genomics approaches. We also discuss some of the available bioinformatics resources for analyzing high-throughput data, in the context of biological pathways and molecular interactions. Although resources for studying host response to infection are available, the corresponding information is lacking for majority of BRD pathogens, impeding progress in identifying diagnostic signatures for BRD using functional genomics approaches.

scholarly journals Supercritical Fluid Extraction of Quinones from Compost for Microbial Community Analysis

2015 ◽  
Vol 2015 ◽  
pp. 1-7
Author(s):  
Ni Luh Gede Ratna Juliasih ◽  
Lee Chang Yuan ◽  
Yuki Sago ◽  
Yoichi Atsuta ◽  
Hiroyuki Daimon
Keyword(s):  
Microbial Community ◽  
Supercritical Fluid Extraction ◽  
Supercritical Fluid ◽  
Community Dynamics ◽  
Community Analysis ◽  
Ultra Performance Liquid Chromatography ◽  
Microbial Community Analysis ◽  
Fluid Extraction ◽  
Dissimilarity Index ◽  
Quinone Profile

Supercritical fluid extraction (SFE) was used to extract quinones from compost to monitor the microbial community dynamics during composting. The 0.3 g of dried compost was extracted using 3 mL min−1of carbon dioxide (90%) and methanol (10%) at 45°C and 25 MPa for a 30 min extraction time. The extracted quinones were analysed using ultra performance liquid chromatography (UPLC) with 0.3 mL min−1of methanol mobile phase for a 50 min chromatographic run time. A comparable detected amount of quinones was obtained using the developed method and an organic solvent extraction method, being 36.06 μmol kg−1and 34.54 μmol kg−1, respectively. Significantly low value of dissimilarity index (D) between the two methods (0.05) indicated that the quinone profile obtained by both methods was considered identical. The developed method was then applied to determine the maturity of the compost by monitoring the change of quinone during composting. The UQ-9 and MK-7 were predominant quinones in the initial stage of composting. The diversity of quinone became more complex during the cooling and maturation stages. This study showed that SFE had successfully extracted quinones from a complex matrix with simplification and rapidity of the analysis that is beneficial for routine analysis.

scholarly journals Spatially varying cis-regulatory divergence inDrosophilaembryos elucidates cis-regulatory logic

2017 ◽  
Author(s):  
Peter A. Combs ◽  
Hunter B. Fraser
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Raw Material ◽  
Spatial Patterning ◽  
Rna Seq ◽  
Specific Expression ◽  
Complex Interactions ◽  
Allele Specific ◽  
Spatially Varying ◽  
Cis And Trans

AbstractSpatial patterning of gene expression is a key process in development—responsible for the incredible diversity of animal body plans—yet how it evolves is still poorly understood. Both cis- and trans-acting changes could accumulate and participate in complex interactions, so to isolate the cis-regulatory component of patterning evolution, we measured allele-specific spatial gene expression patterns inD. melanogaster×D. simulanshybrid embryos. RNA-seq of cryosectioned slices revealed 55 genes with strong spatially varying allele-specific expression, and several hundred more with weaker but significant spatial divergence. For example, we found thathunchback (hb), a major regulator of developmental patterning, had reduced expression specifically in the anterior tip ofD. simulansembryos. Mathematical modeling ofhbcis-regulation suggested that a mutation in a Bicoid binding site was responsible, which we verified using CRISPR-Cas9 genome editing. In sum, even comparing morphologically near-identical species we identified a substantial amount of spatial variation in gene expression, suggesting that development is robust to many such changes, but also that natural selection may have ample raw material for evolving new body plans via cis-regulatory divergence.

Missing data in open-data era – a barrier to multiomics integration

2018 ◽  
Vol 14 (1) ◽  
Author(s):  
Monika Piwowar ◽  
Wiktor Jurkowski
Keyword(s):  
Quantitative Data ◽  
Open Data ◽  
Multidimensional Data ◽  
Data Sets ◽  
Biological Processes ◽  
Rna Seq ◽  
Data Set ◽  
Complex Interactions ◽  
Integrate Data ◽  
Generation Sequencing

AbstractThe exploration of complex interactions in biological systems is one of the main aims in nature science nowadays. Progress in this area is possible because of high-throughput omics technologies and the computational surge. The development of analytical methods “is trying to keep pace” with the development of molecular biology methods that provide increasingly large amounts of data – omics data. Specialized databases consist of ever-larger collections of experiments that are usually conducted by one next-generation sequencing technique (e.g. RNA-seq). Other databases integrate data by defining qualitative relationships between individual objects in the form of ontologies, interactions, and pathways (e.g. GO, KEGG, and String). However, there are no open-source complementary quantitative data sets for the biological processes studied, including information from many levels of the organism organization, which would allow the development of multidimensional data analysis methods (multiscale and insightful overviews of biological processes). In the paper, the lack of omics complementary quantitative data set, which would help integrate the defined qualitative biological relationships of individual biomolecules with statistical, computational methods, is discussed.

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