When trees die: Understanding how plants and microbes interact and influence soil biogeochemical processes
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PROVIDER: PRJEB64633 | ENA |
REPOSITORIES: ENA
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Project description:An estimated three million shipwrecks exist worldwide and are recognized as cultural resources and foci of archaeological investigations. Shipwrecks also support ecological resources by providing underwater habitats that can be colonized by diverse organisms ranging from microbes to megafauna. In the present article, we review the emerging ecological subdiscipline of shipwreck ecology, which aims to understand ecological functions and processes that occur on shipwrecks. We synthesize how shipwrecks create habitat for biota across multiple trophic levels and then describe how fundamental ecological functions and processes, including succession, zonation, connectivity, energy flow, disturbance, and habitat degradation, manifest on shipwrecks. We highlight future directions in shipwreck ecology that are ripe for exploration, placing a particular emphasis on how shipwrecks may serve as experimental networks to address long-standing ecological questions.
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Project description:Alkalinity, the excess of proton acceptors over donors, plays a major role in ocean chemistry, in buffering and in calcium carbonate precipitation and dissolution. Understanding alkalinity dynamics is pivotal to quantify ocean carbon dioxide uptake during times of global change. Here we review ocean alkalinity and its role in ocean buffering as well as the biogeochemical processes governing alkalinity and pH in the ocean. We show that it is important to distinguish between measurable titration alkalinity and charge balance alkalinity that is used to quantify calcification and carbonate dissolution and needed to understand the impact of biogeochemical processes on components of the carbon dioxide system. A general treatment of ocean buffering and quantification via sensitivity factors is presented and used to link existing buffer and sensitivity factors. The impact of individual biogeochemical processes on ocean alkalinity and pH is discussed and quantified using these sensitivity factors. Processes governing ocean alkalinity on longer time scales such as carbonate compensation, (reversed) silicate weathering, and anaerobic mineralization are discussed and used to derive a close-to-balance ocean alkalinity budget for the modern ocean.
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Project description:Migratory marine vertebrates move annually across remote oceanic water masses crossing international borders. Many anthropogenic threats such as overfishing, bycatch, pollution or global warming put millions of marine migrants at risk especially during their long-distance movements. Therefore, precise knowledge about these migratory movements to understand where and when these animals are more exposed to human impacts is vital for addressing marine conservation issues. Because electronic tracking devices suffer from several constraints, mainly logistical and financial, there is emerging interest in finding appropriate intrinsic markers, such as the chemical composition of inert tissues, to study long-distance migrations and identify wintering sites. Here, using tracked pelagic seabirds and some of their own feathers which were known to be grown at different places and times within the annual cycle, we proved the value of biogeochemical analyses of inert tissue as tracers of marine movements and habitat use. Analyses of feathers grown in summer showed that both stable isotope signatures and element concentrations can signal the origin of breeding birds feeding in distinct water masses. However, only stable isotopes signalled water masses used during winter because elements mainly accumulated during the long breeding period are incorporated into feathers grown in both summer and winter. Our findings shed new light on the simple and effective assignment of marine organisms to distinct oceanic areas, providing new opportunities to study unknown migration patterns of secretive species, including in relation to human-induced mortality on specific populations in the marine environment.
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Project description:The abundance of the divaricate growth form in New Zealand has been interpreted as either (a) the response of an isolated flora to cool, dry, Plio-Pleistocene climates; or (b) a defense against large browsing birds (moa) that were hunted to extinction shortly after human arrival during the last millennium. We used patterns of divaricate plant abundance across present-day landscapes to test a novel synthetic hypothesis: that the divaricate form is of most value to plants on fertile soils that attract herbivores, on sites where climatic constraints prevent plants from quickly growing out of the browse zone. This hypothesis predicts that divaricate species should be most abundant on terraces (landforms that are both fertile and frost-prone) in regions that are cold and dry, and should be scarce across all topographic positions in the warmest (largely frost-free) regions. To address our hypothesis, we first tested the influence of topography on frost regimes and nutrient levels by measuring temperatures and soil total C, N, and P at four standard topographic positions at five localities differing widely in macroclimate. We then extracted a dataset of 236 surveys comprising 9,877 relevé plots from the New Zealand National Vegetation Survey databank. We calculated the proportion of arborescent species with a divaricate growth form and the proportion of total arborescentcover contributed by divaricates on each plot; we then fitted linear mixed-effect models predicting these response variables as functions of topographic position and climate. The number of frosts recorded averaged <1 yr-1 at the warmest of the five sites studied, to >60 yr-1 on all topographic positions at the coldest site. Terraces were subject to more frequent and harder frosts than any other topographic position. Topography had no significant influence on total N or C:N, but total P was higher on terraces and in gullies than on faces or ridges. Frost-free period was the dominant influence on both species representation and cover of divaricate plants throughout the country. The effect of topography was also significant, but weaker. The effect of frost-free period was stronger on sites with water deficits than on sites where precipitation exceeded evapotranspiration. Divaricates made their largest contributions on terraces in cold, dry regions; as predicted, they were scarce on all topographic positions on sites with frost-free periods >300 days. Our hypothesis was generally supported, although the effect of topography on divaricate abundance was not as strong as some previous studies led us to expect. Divaricates made their largest contributions to arborescent species richness and cover on sites where climatic restrictions on growth coincide with relatively high nutrient availability. The contemporary distribution of the divaricate form across New Zealand landscapes thus appears to be reasonably well explained by the hypothesized interaction of climate and fertility-mediated browsing, although experiments may provide more conclusive tests of this hypothesis.
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Project description:The Earth's subsurface represents a complex electrochemical environment that contains many electro-active chemical compounds that are relevant for a wide array of biologically driven ecosystem processes. Concentrations of many of these electro-active compounds within Earth's subsurface environments fluctuate during the day and over seasons. This has been observed for surface waters, sediments and continental soils. This variability can affect particularly small, relatively immobile organisms living in these environments. While various drivers have been identified, a comprehensive understanding of the causes and consequences of spatio-temporal variability in subsurface electrochemistry is still lacking. Here we propose that variations in atmospheric electricity (AE) can influence the electrochemical environments of soils, water bodies and their sediments, with implications that are likely relevant for a wide range of organisms and ecosystem processes. We tested this hypothesis in field and laboratory case studies. Based on measurements of subsurface redox conditions in soils and sediment, we found evidence for both local and global variation in AE with corresponding patterns in subsurface redox conditions. In the laboratory, bacterial respiratory responses, electron transport activity and H2S production were observed to be causally linked to changes in atmospheric cation concentrations. We argue that such patterns are part of an overlooked phenomenon. This recognition widens our conceptual understanding of chemical and biological processes in the Earth's subsurface and their interactions with the atmosphere and the physical environment.
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Project description:Gene body methylation (gbM) is an epigenetic mark where gene exons are methylated in the CG context only, as opposed to CHG and CHH contexts (where H stands for A, C, or T). CG methylation is transmitted transgenerationally in plants, opening the possibility that gbM may be shaped by adaptation. This presupposes, however, that gbM has a function that affects phenotype, which has been a topic of debate in the literature. Here, we review our current knowledge of gbM in plants. We start by presenting the well-elucidated mechanisms of plant gbM establishment and maintenance. We then review more controversial topics: the evolution of gbM and the potential selective pressures that act on it. Finally, we discuss the potential functions of gbM that may affect organismal phenotypes: gene expression stabilization and upregulation, inhibition of aberrant transcription (reverse and internal), prevention of aberrant intron retention, and protection against TE insertions. To bolster the review of these topics, we include novel analyses to assess the effect of gbM on transcripts. Overall, a growing body of literature finds that gbM correlates with levels and patterns of gene expression. It is not clear, however, if this is a causal relationship. Altogether, functional work suggests that the effects of gbM, if any, must be relatively small, but there is nonetheless evidence that it is shaped by natural selection. We conclude by discussing the potential adaptive character of gbM and its implications for an updated view of the mechanisms of adaptation in plants.
| S-EPMC8995044 | biostudies-literature
Project description:The atmosphere of the early Earth is hypothesized to have been rich in reducing gases such as hydrogen (H2). H2 has been proposed as the first electron donor leading to ATP synthesis due to its ubiquity throughout the biosphere as well as its ability to easily diffuse through microbial cells and its low activation energy requirement. Even today, hydrogenase enzymes enabling the production and oxidation of H2 are found in thousands of genomes spanning the three domains of life across aquatic, terrestrial, and even host-associated ecosystems. Even though H2 has already been proposed as a universal growth and maintenance energy source, its potential contribution as a driver of biogeochemical cycles has received little attention. Here, we bridge this knowledge gap by providing an overview of the classification, distribution, and physiological role of hydrogenases. Distribution of these enzymes in various microbial functional groups and recent experimental evidence are finally integrated to support the hypothesis that H2-oxidizing microbes are keystone species driving C cycling along O2 concentration gradients found in H2-rich soil ecosystems. In conclusion, we suggest focusing on the metabolic flexibility of H2-oxidizing microbes by combining community-level and individual-level approaches aiming to decipher the impact of H2 on C cycling and the C-cycling potential of H2-oxidizing microbes, via both culture-dependent and culture-independent methods, to give us more insight into the role of H2 as a driver of biogeochemical processes.
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Project description:After a century of incremental research, technological advances, coupled with a need for sustainable crop yield increases, have reinvigorated the study of beneficial plant-microbe interactions with attention focused on how microbiomes alter plant phenotypes. We review recent advances in plant microbiome research, and describe potential applications for increasing crop productivity. The phylogenetic diversity of plant microbiomes is increasingly well characterized, and their functional diversity is becoming more accessible. Large culture collections are available for controlled experimentation, with more to come. Genetic resources are being brought to bear on questions of microbiome function. We expect that microbial amendments of varying complexities will expose rules governing beneficial plant-microbe interactions contributing to plant growth promotion and disease resistance, enabling more sustainable agriculture.
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Project description:Grapevine is a perennial crop often cultivated by grafting a scion cultivar on a suitable rootstock. Rootstocks influence scions, particularly with regard to water uptake and vigor. Therefore, one of the possibilities to adapt viticulture to the extended drought stress periods is to select rootstocks conferring increased tolerance to drought. However, the molecular mechanisms associated with the ability of rootstock/scion combination to influence grape berry metabolism under drought stress are still poorly understood. The transcriptomic changes induced by drought stress in grape berries (cv. Pinot noir) from vines grafted on either 110R (drought tolerant) or 125AA (drought sensitive) rootstock were compared. The experiments were conducted in the vineyard for two years and two grape berry developmental stages (50% and 100 % veraison. The genome-wide microarray approach showed that water stress strongly impacts gene expression in the berries, through ontology categories that cover cell wall metabolism, primary and secondary metabolism, signalling, stress, and hormones, and that some of these effects strongly depend on the rootstock genotype. Indeed, under drought stress, berries from vines grafted on 110R displayed a different transcriptional response compared to 125AA concerning genes related to jasmonate, phenylpropanoid metabolism and PR-proteins. The data also suggests a link between jasmonate and secondary metabolism in water-stressed berries. Overall, genes related to secondary metabolism and jasmonate are more induced and/or less repressed by drought stress in the berries grafted on the drought-sensitive rootstock 125AA. These rootstock-dependent gene expression changes are relevant for berry composition and sensory properties.
2015-03-19 | GSE66391 | GEO
Project description:The impact of otter trawling on the relationship between functional traits of benthic invertebrates and specific biogeochemical processes were investigated in the oligotrophic Cretan Sea. The fishery is managed through a seasonal closure during the summer. During two seasons (winter and summer) replicate samples were taken from the field from a commercial trawl ground and an adjacent control area. Environmental parameters related to sediment biogeochemistry were measured including particulate organic carbon, sedimentary organic carbon, bottom water and sedimentary chlorophyll a and phaeopigment concentrations as well as benthic oxygen consumption. A significant impact of trawling was recorded only for bottom water chlorophyll and sedimentary organic carbon. Furthermore, the links between species traits and specific ecosystem processes were affected by trawling, highlighting the importance of unique functional modalities on ecosystem functioning. The traits that mostly influenced benthic biogeochemistry in the control sites were related to bioturbation and burrowing activities. In contrast, in the trawled sites, the associated traits were related to more opportunistic lifestyles and deposit feeding species that do not act as bioturbators. Thus, under trawling disturbance, this shift can decouple the species-sediment relations and affect nutrient cycling.
| S-EPMC9598213 | biostudies-literature