Elife , IF:7.08 , 2019 Nov , V8 doi: 10.7554/eLife.52123
Life on a leaf.
Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland.
Microscopic water films allow bacteria to survive the seemingly dry surface of plant leaves.
PMID: 31674912
Mol Ecol Resour , IF:6.286 , 2019 Nov , V19 (6) : P1565-1577 doi: 10.1111/1755-0998.13081
Interdomain ecological networks between plants and microbes.
CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.; Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Key Laboratory of Forest Ecology and Environment of State Forestry Administration, Beijing, China.; Environmental Microbiomics Research Center, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.; Institute for Environmental Genomics, Department of Microbiology and Plant Biology, School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.
While macroscopic interkingdom relationships have been intensively investigated in various ecosystems, the above-belowground ecology in natural ecosystems has been poorly understood, especially for the plant-microbe associations at a regional scale. In this study, we proposed a workflow to construct interdomain ecological networks (IDEN) between multiple plants and various microbes (bacteria and archaea in this study). Across 30 latitudinal forests in China, the regional IDEN showed particular topological features, including high connectance, nested structure, asymmetric specialization and modularity. Also, plant species exhibited strong preference to specific microbial groups, and the observed network was significantly different from randomly rewired networks. Network module analysis indicated that a majority of microbes associated with plants within modules rather than across modules, suggesting specialized associations between plants and microorganisms. Consistent plant-microbe associations were captured via IDENs constructed within individual forest locations, which reinforced the validity of IDEN analysis. In addition, the plant-forest link distribution showed the geographical distribution of plants had higher endemicity than that of microorganisms. With cautious experimental design and data processing, this study shows interdomain species associations between plants and microbes in natural forest ecosystems and provides new insights into our understanding of meta-communities across different domain species.
PMID: 31479575
Chemosphere , IF:5.778 , 2019 Nov , V235 : P248-259 doi: 10.1016/j.chemosphere.2019.06.174
Dominant role of abundant rather than rare bacterial taxa in maintaining agro-soil microbiomes under environmental disturbances.
State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China; College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China. Electronic address: chenwm029@nwsuaf.edu.cn.; College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China. Electronic address: luyh@pku.edu.cn.
Elucidating the mechanisms underpinning the responses of abundant and rare microbial taxa to environmental disturbances is essential for understanding the biodiversity-stability relationship and maintaining microbial diversity. Here, we explored the response patterns of abundant and rare bacterial taxa to disturbances by invasive plant growth and oil contamination in agricultural soils across a large spatial scale (latitude gradient=18.62 degrees -46.51 degrees ). Our meta-analysis based on existing Illumina sequencing datasets showed that abundant taxa persisted under the disturbances whereas rare taxa were more easily affected, indicating the higher resilience or resistance of abundant taxa to disturbances. The responses of abundant taxa were associated with mean annual temperature at the sampling sites, while rare taxa instead showed stochastic responses. There were significantly negative linear regressions between bacterial alpha-diversity and community dissimilarities (disturbed vs. undisturbed soils), suggesting stronger resilience or resistance in those bacterial communities with higher alpha-diversity. This resilience or resistance was mainly associated with the alpha-diversity of abundant taxa. Our network analysis showed that the disturbances substantially decreased the strength of the connections, loosened the co-occurrence relationships, and reshaped the complex bacterial interactions. In the undisturbed soils, abundant taxa were located in central positions within the network more often than were rare taxa, while these trends were reversed in the disturbed soils. Our results suggest that abundant taxa play a dominant role in the stability and maintenance of agro-soil bacterial communities, while rare taxa could greatly influence local bacterial interactions under environmental disturbances.
PMID: 31260865
Plant Cell Physiol , IF:4.062 , 2019 Nov , V60 (11) : P2464-2477 doi: 10.1093/pcp/pcz139
Evolution of Lineage-Specific Gene Networks Underlying the Considerable Fruit Shape Diversity in Persimmon.
Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.; Japan Science and Technology Agency (JST), PRESTO, Kawaguchi-shi, Saitama, Japan.; Institute of Fruit Tree and Tea Science, NARO, Higashihiroshima, Japan.
The shapes of plant organs reflect the evolution of each lineage and have been diversified according to lineage-specific adaptations to environment. Research on the molecular pathways responsible for organ shapes has traditionally been focused mainly on leaves or flowers. Thus, little is known about the pathways controlling fruit shapes, despite their diversity in some plant species. In this study, we analyzed oriental persimmon (Diospyros kaki), which exhibits considerable diversity in fruit shapes among cultivars, to elucidate the underlying molecular mechanism using transcriptomic data and quantitative evaluation. First, to filter the candidate genes associated with persimmon fruit shapes, the whole gene expression patterns obtained using mRNA-Seq analysis from 100 individuals, including a segregated population and various cultivars, were assessed to detect correlations with principal component scores for fruit shapes characterized with elliptic Fourier descriptors. Next, a gene co-expression network analysis with weighted gene co-expression network analysis (WGCNA) package revealed that class 1 KNOX family genes and SEEDSTICK function as integrators along with some phytohormone-related genes, to regulate the fruit shape diversity. On the other hand, the OVATE family genes also contribute to fruit shape diversity, of which pathway would be potentially shared with other plant species. Evolutionary aspects suggest that acquisition of a high lineage-specific and variable expression of class 1 KNOX gene, knotted-like homeobox of Arabidopsis thaliana 1 (KNAT1), in young fruit is important for establishing the persimmon-specific mechanism that determines fruit shape diversity.
PMID: 31350891
BMC Plant Biol , IF:3.497 , 2019 Nov , V19 (1) : P516 doi: 10.1186/s12870-019-2125-z
PI signal transduction and ubiquitination respond to dehydration stress in the red seaweed Gloiopeltis furcata under successive tidal cycles.
Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China.; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China.; University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.; Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China. huzm@qdio.ac.cn.; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China. huzm@qdio.ac.cn.; Ocean School, Yantai University, Yantai, 264005, People's Republic of China.; Verschuren Centre for Sustainability in Energy and Environment, University of Cape Breton, Sydney, Nova Scotia, Canada.; Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China. dlduan@qdio.ac.cn.; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China. dlduan@qdio.ac.cn.
BACKGROUND: Intermittent dehydration caused by tidal changes is one of the most important abiotic factors that intertidal seaweeds must cope with in order to retain normal growth and reproduction. However, the underlying molecular mechanisms for the adaptation of red seaweeds to repeated dehydration-rehydration cycles remain poorly understood. RESULTS: We chose the red seaweed Gloiopeltis furcata as a model and simulated natural tidal changes with two consecutive dehydration-rehydration cycles occurring over 24 h in order to gain insight into key molecular pathways and regulation of genes which are associated with dehydration tolerance. Transcription sequencing assembled 32,681 uni-genes (GC content = 55.32%), of which 12,813 were annotated. Weighted gene co-expression network analysis (WGCNA) divided all transcripts into 20 modules, with Coral2 identified as the key module anchoring dehydration-induced genes. Pathways enriched analysis indicated that the ubiquitin-mediated proteolysis pathway (UPP) and phosphatidylinositol (PI) signaling system were crucial for a successful response in G. furcata. Network-establishing and quantitative reverse transcription PCR (qRT-PCR) suggested that genes encoding ubiquitin-protein ligase E3 (E3-1), SUMO-activating enzyme sub-unit 2 (SAE2), calmodulin (CaM) and inositol-1,3,4-trisphosphate 5/6-kinase (ITPK) were the hub genes which responded positively to two successive dehydration treatments. Network-based interactions with hub genes indicated that transcription factor (e.g. TFIID), RNA modification (e.g. DEAH) and osmotic adjustment (e.g. MIP, ABC1, Bam1) were related to these two pathways. CONCLUSIONS: RNA sequencing-based evidence from G. furcata enriched the informational database for intertidal red seaweeds which face periodic dehydration stress during the low tide period. This provided insights into an increased understanding of how ubiquitin-mediated proteolysis and the phosphatidylinositol signaling system help seaweeds responding to dehydration-rehydration cycles.
PMID: 31771523
BMC Plant Biol , IF:3.497 , 2019 Nov , V19 (1) : P463 doi: 10.1186/s12870-019-2074-6
Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species.
The ministry of agriculture of Qinghai-Tibet plateau fruit trees scientific observation test station, Lhasa, 850032, Tibet, China.; Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, Tibet, China.; Wuhan Metware Biotechnology Co., Ltd, Wuhan, 430070, China.; The ministry of agriculture of Qinghai-Tibet plateau fruit trees scientific observation test station, Lhasa, 850032, Tibet, China. zeng_xiuli2008@aliyun.com.; Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, Tibet, China. zeng_xiuli2008@aliyun.com.
BACKGROUND: Flesh color is one of the most important traits for the commercial value of peach fruit. To unravel the underlying regulatory network in Prunus mira, we performed an integrated analysis of the transcriptome and metabolome of 3 fruit types with various flesh pigmentations (milk-white, yellow and blood) at 3 developmental stages (pit-hardening, cell enlargement and fruit ripening). RESULTS: Transcriptome analysis showed that an intense transcriptional adjustment is required for the transition from the pit-hardening to the cell enlargement stage. In contrast, few genes were differentially expressed (DEGs) from the cell enlargement to the fruit ripening stage and importantly, the 3 fruits displayed diverse transcriptional activities, indicating that difference in fruit flesh pigmentations mainly occurred during the ripening stage. We further investigated the DEGs between pairs of fruit types during the ripening stage and identified 563 DEGs representing the 'core transcriptome' associated with major differentiations between the 3 fruit types, including flesh pigmentation. Meanwhile, we analyzed the metabolome, particularly, at the ripening stage and uncovered 40 differential metabolites ('core metabolome') between the 3 fruit types including 5 anthocyanins, which may be the key molecules associated with flesh coloration. Finally, we constructed the regulatory network depicting the interactions between anthocyanins and important transcripts involved in fruit flesh coloration. CONCLUSIONS: The major metabolites and transcripts involved in fruit flesh coloration in P. mira were unraveled in this study providing valuable information which will undoubtedly assist in breeding towards improved fruit quality in peach.
PMID: 31675926
Microb Ecol , IF:3.356 , 2019 Nov , V78 (4) : P949-960 doi: 10.1007/s00248-019-01367-x
A Polyphasic Approach for Assessing Eco-System Connectivity Demonstrates that Perturbation Remodels Network Architecture in Soil Microcosms.
International Hellenic University, 14th km Thessaloniki-N. Moudania, 57001 Thermi, Thessaloniki, Greece.; Department of Soil Science of Athens, Institute of Soil and Water Resources, Hellenic Agricultural Organization-DEMETER, 14123, Athens, Greece.; Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Ceredigion, UK.; International Hellenic University, 14th km Thessaloniki-N. Moudania, 57001 Thermi, Thessaloniki, Greece. papatheo@bio.auth.gr.; Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece. papatheo@bio.auth.gr.
Network analysis was used to show changes in network attributes by analyzing the relations among the main soil microbial groups in a potted tomato soil inoculated with arbuscular mycorrhizal fungus, treated with low doses of Mentha spicata essential oil, or both, and then exposed to tenfold higher oil addition (stress pulse). Pretreatments were chosen since they can induce changes in the composition of the microbial community. Cellular phospholipid fatty acids (PLFAs) and the activity of six soil enzymes, mainly involved in the N-cycle were measured. Networks were constructed based on correlated changes in PLFA abundances. The values of all parameters were significantly different from those of random networks indicating modular architecture. Networks ranked from the lowest to highest modularity: control, non-pretreated and stressed, inoculated and stressed, oil treated and stressed, inoculated and treated with oil and stressed. The high values of network density and 1st/2nd eigenvalue ratio are related to arylamidase activity while N-acetyl-glucosaminidase, acid phosphomoesterase, and asparaginase activities related to high values of the clustering coefficient index. We concluded that modularity may be an efficient indicator of changes in the network of interactions among the members of the soil microbial community and the modular structure of the network may be related to the activity of specific enzymes. Communities that were stressed without a pretreatment were relatively resistant but prone to sudden transition towards instability, while oil or inoculation pretreatments gave networks which could be considered adaptable and susceptible to gradual change.
PMID: 30953090
Appl Ergon , IF:3.145 , 2019 Nov , V81 : P102904 doi: 10.1016/j.apergo.2019.102904
Who is responsible for automated driving? A macro-level insight into automated driving in the United Kingdom using the Risk Management Framework and Social Network Analysis.
Human Factors Engineering, Transportation Research Group, Faculty of Engineering and Physical Sciences, University of Southampton, SO16 7QF, UK. Electronic address: v.banks@soton.ac.uk.; Human Factors Engineering, Transportation Research Group, Faculty of Engineering and Physical Sciences, University of Southampton, SO16 7QF, UK.
To date, vehicle manufacturers have largely been left to their own initiatives when it comes to the design, development and implementation of automated driving features. Whilst this has enabled developments within the field to accelerate at a rapid pace, we are also now beginning to see the negative aspects of automated design (e.g., driver complacency, automation misuse and ethical dilemmas). It is therefore becoming increasingly important to identify systemic aspects that can address some of these Human Factors challenges. This paper applies the principles of the Risk Management Framework to explore the wider systemic issues associated with automated driving in the United Kingdom through the novel application of network metrics. The authors propose a number of recommendations targeted at each level of the Risk Management Framework that seek to shift the power of influence away from vehicle manufacturers and back into the hands of governing bodies.
PMID: 31422264
Br J Math Stat Psychol , IF:2.388 , 2019 Nov doi: 10.1111/bmsp.12192
Deterministic blockmodelling of signed and two-mode networks: A tutorial with software and psychological examples.
Florida State University, Tallahassee, Florida, USA.; University of Ljubljana, Ljubljana, Slovenia.; Univerity of Pittsburgh, Pittsburgh, Pennsylvania, USA.; University of Missouri, Columbia, Missouri, USA.
Deterministic blockmodelling is a well-established clustering method for both exploratory and confirmatory social network analysis seeking partitions of a set of actors so that actors within each cluster are similar with respect to their patterns of ties to other actors (or, in some cases, other objects when considering two-mode networks). Even though some of the historical foundations for certain types of blockmodelling stem from the psychological literature, applications of deterministic blockmodelling in psychological research are relatively rare. This scarcity is potentially attributable to three factors: a general unfamiliarity with relevant blockmodelling methods and applications; a lack of awareness of the value of partitioning network data for understanding group structures and processes; and the unavailability of such methods on software platforms familiar to most psychological researchers. To tackle the first two items, we provide a tutorial presenting a general framework for blockmodelling and describe two of the most important types of deterministic blockmodelling applications relevant to psychological research: structural balance partitioning and two-mode partitioning based on structural equivalence. To address the third problem, we developed a suite of software programs that are available as both Fortran executable files and compiled Fortran dynamic-link libraries that can be implemented in the R software system. We demonstrate these software programs using networks from the literature.
PMID: 31705539