Abiotic Processes Research Articles

In-depth assembly of organ and development dissected Picrorhiza kurroa proteome map using mass spectrometry

BackgroundPicrorhiza kurroa Royle ex Benth. being a rich source of phytochemicals, is a promising high altitude medicinal herb of Himalaya. The medicinal potential is attributed to picrosides i.e. iridoid glycosides, which synthesized in organ-specific manner through highly complex pathways. Here, we present a large-scale proteome reference map of P. kurroa, consisting of four morphologically differentiated organs and two developmental stages.ResultsWe were able to identify 5186 protein accessions (FDR < 1%) providing a deep coverage of protein abundance array, spanning around six orders of magnitude. Most of the identified proteins are associated with metabolic processes, response to abiotic stimuli and cellular processes. Organ specific sub-proteomes highlights organ specialized functions that would offer insights to explore tissue profile for specific protein classes. With reference to P. kurroa development, vegetative phase is enriched with growth related processes, however generative phase harvests more energy in secondary metabolic pathways. Furthermore, stress-responsive proteins, RNA binding proteins (RBPs) and post-translational modifications (PTMs), particularly phosphorylation and ADP-ribosylation play an important role in P. kurroa adaptation to alpine environment. The proteins involved in the synthesis of secondary metabolites are well represented in P. kurroa proteome. The phytochemical analysis revealed that marker compounds were highly accumulated in rhizome and overall, during the late stage of development.ConclusionsThis report represents first extensive proteomic description of organ and developmental dissected P. kurroa, providing a platform for future studies related to stress tolerance and medical applications.

Ecosystem models indicate zooplankton biomass response to nutrient input and climate warming is related to lake size

Zooplankton is an essential part of the simulation in ecological process-based models and rigorous calibration of the zooplankton module lacks relevant modeling research that can predict the response of zooplankton biomass to varied environmental factors. The paper therefore builds a one-dimensional lake ecology model PCLake, which quantifies the dynamic effects on zooplankton in small water bodies distinguished by lake size and eutrophication status in warming climates. Based on the main geometric characteristics among a series of shallow water bodies, we constructed three lake models, namely, a northern lake with a larger area (> 0.1 ha) in Poland (Lake NL), a northern lake with a smaller (< 0.1 ha) area in Poland (Lake NS), and a southern lake with the smallest area in Croatia (Lake SS). Data from 2017 to 2018, including water temperature, dissolved oxygen (DO), total nitrogen (TN), total phosphorus (TP), chlorophyll a (Chl a), and zooplankton, were used to calibrate and verify models for three shallow water body categories and uncertainty analyses were carried out to support the credibility of our models. Further, to discuss the potential driving forces of environmental factors on zooplankton, we set up a series of scenarios in which atmospheric temperature and nutrient input were changed. Zooplankton are only considered as a common pool and therefore only how biomass varied can be obtained. Warming resulted in a decline of zooplankton in the lakes located in Northern Europe, with peak decreases in zooplankton biomass more than four times higher in Lake NS than in Lake NL. In addition, due to multiple nutrient loading scenarios, incoming nitrogen and phosphorus concentrations were found to have a huge impact on zooplankton biomass in Lake NL. Specifically, relative to the original eutrophic level, the average annual biomass of zooplankton increased by 90% with a 75% increase in organic nitrogen over the original eutrophic level and decreased by more than 50% with a 75% decrease in inorganic phosphorus. Hence, lake size characteristics should be taken into account in management and restoration as they may be synergistic with in-lake biological and abiotic processes under complex environmental forces.

Arbuscular mycorrhizal fungi outcompete fine roots in determining soil multifunctionality and microbial diversity in a desert ecosystem

Fine roots and mycorrhizal fungi play a crucial role in soil nutrient cycling and microbial processes. However, the importance of the symbioses between fine roots and arbuscular mycorrhizal fungi (AMF) in different plant functional groups to maintain soil multifunctionality (the ability to provide multiple functions and services) and microbial diversity remains unclear, especially in desert ecosystems. In this study, we conducted an ingrowth core experiment on three vegetation types, namely shrub-dominated, grass-dominated, and mixed vegetation communities, in the Mu Us Desert, northern China, to investigate the importance of fine roots and mycorrhizal fungi in shaping soil nutrient composition and microbiome. Furthermore, we detected the relationships among AMF-related inputs [extraradical AMF hyphae and glomalin-related soil protein (GRSP)], soil multifunctionality, and soil microbial diversity. We found that most of the soil properties associated with nutrient cycling and microbial community composition and diversity varied among the three vegetation types, but were not significantly different between distinct ingrowth core treatments with fine root and hyphal access. AMF-related inputs, especially the easily extractable GRSP, were the most important determinants of soil multifunctionality and microbial community diversity across the shrub and grass communities, while the changes in soil multifunctionality and microbial diversity were inconsistent with the trend of fine root biomass. Moreover, AMF-related inputs were positively correlated with soil nutrients, particularly soil organic carbon (SOC). In contrast to the minimal negative correlation between SOC and soil microbial richness, soil multifunctionality was positively correlated with SOC. These findings support the role of AMF in shaping soil multifunctionality and microbial diversity by stabilizing SOC in a desert ecosystem, regardless of the fine root accessibility of plant functional groups. Therefore, this study improved our understanding of plant-derived carbon in the soil and its effects on the induction of soil abiotic and biotic processes in resource-limited ecosystems.

DOONIES: A process-based ecogeomorphological functional community model for coastal dune vegetation and landscape dynamics

In ecogeomorphic systems, such as beach-dune habitats, complex couplings exist between geomorphology and ecology. Abiotic conditions influence vegetation growth and distribution while vegetation imposes a geomorphic feedback, impacting topography. Communities affect storm response by impacting pre-storm state, post-storm recovery, and landscape evolution. Despite their importance, beach-dune and other ecogeomorphic land-sea systems are deteriorating with increased anthropogenic modification and amplified natural disaster impact linked to climate change. A structured approach is needed to develop a more comprehensive understanding of coastal vegetation community interactions with the environment as these interactions underpin topographic change, strom response, and restoration and management efforts. Toward this goal, a spatially explicit process-based grid model, the DOONIES Model, encompassing biological, physiological, and geomorphological drivers of landscape change is presented. DOONIES simulates critical biotic and abiotic processes of vegetation growth, abundance, and spatial distribution dynamics impacting topography and storm response. Biological processes and ecogeomorphic responses are tailored to generalizable dune functional-communities with species-specific representatives. Estimates of the balance between photosynthesis and respiration dictate plant growth and morphology spatiotemporally which in turn impact sediment erosion and deposition. Relative sensitivity analyses indicate that the model is fundamentally driven by the photosynthesis formulation, where parameters such as maximum daily photosynthesis (grams of carbohydrate per day) and light intensity impact vegetation growth. These in turn, indirectly impact topographic change in modeled ecogeomorphic links. DOONIES is standalone and with a biological focus making it unique compared to more physical morphodynamic and hydrodynamic models with which this model is designed to couple. The model was evaluated by comparing simulation topography to actual across 6 years at Island Beach State Park, NJ while modeling Hurricane Sandy and daily wind conditions driving sediment input and output events. The predicted results were within the measurement error for the elevation datasets that the simulations were based on. This new model affords dynamic predictions of the response of naturally occurring and planted dune vegetation communities to typical abiotic conditions, as a tool for supporting and exploring restoration decisions.

Carbon stocks in umbric ferralsols driven by plant productivity and geomorphic processes, not by mineral protection

AbstractUmbric ferralsols (UF) have organic carbon stocks within the first 1 m of soil profile depth that are nearly double the size (~19 kg C m−2) compared to the average carbon stocks of all other ferralsols (~10 kg C m−2). Here, we investigate processes that allow UF to gain and maintain such extraordinary carbon stocks. Using the International Soil Research and Information Center database, complemented with recently published datasets, we show that the carbon saturation capacity of the clay + silt fractions in UF (22.8 ± 5.7 g C kg−1 soil, n = 59) does not exceed the carbon saturation capacity in other ferralsols (23.3 ± 6.2 g C kg−1 soil, n = 165), thus eliminating a particularly retentive mineral matrix as a possible explanation. Rather, carbon stocks were correlated with the thickness of A horizons (106 ± 49 cm, n = 59 in umbric versus 35 ± 22 cm, n = 165 in non‐umbric ferralsols). We subsequently hypothesized that differences in A‐horizon thickness arose from two pedogenic scenarios: (i) superior carbon accrual resulting from a unique vegetation cover capable of allocating large quantities of carbon to belowground plant organs; and (ii) geomorphic processes that led to carbon burial. We evaluated the plausibility of these scenarios considering landscape history and associated carbon flux rates, hillslope position, as well as δ13C values and Ti/Zr ratios for subsets of ferralsol profiles studied by us in a region that encompasses latitudes from 26 to 7°S in eastern Brazil. We found that exceptional carbon stocks were most prevalent in the gradual transition zone (ecotone) between savanna and rainforest, likely resulting from erosion–deposition processes, historic changes of vegetation cover composed of grasses and arboreal elements, and active bioturbation. We suggest that attempts to sequester carbon in non‐umbric ferralsols will be most successful if they emulate or promote the biotic and abiotic processes prevalent in the savanna/rainforest ecotone.

Biotic and abiotic factors control the geomorphic characteristics of channel networks in salt marshes

AbstractBiotic and abiotic processes control the formation and evolution of tidal channel networks. However, which factor regulates the planimetric geometry of the network remains unclear. Here, we compare the geometric properties of tidal channel networks in 14 salt marshes along the coasts of the United States and China. Significant difference in the geometric properties of tidal channel networks was found in salt marshes dominated by different vegetation species. Physical parameters better explained these differences, while vegetation parameters had a weaker effect on the network geometry. Mean marsh elevation and tidal range were found to be the best variables to explain the variability in drainage density, mean unchanneled path length and sinuosity (R2 values range from 0.239 to 0.465), while biotic parameters (i.e., aboveground biomass, stem density, height, and diameter) were only significant predictors for less geometric properties (R2 values range from 0.005 to 0.312). We used multiple regressions to develop sample models, explaining more than 60% of the variability in mean unchanneled path length. Our findings underline the key role of physical factors in shaping tidal channel networks. We conclude that physical processes are more important than vegetation species in determining the long‐term development of tidal channels.

Shotgun metagenomics evaluation of soil fertilization effect on the rhizosphere viral community of maize plants.

The need for sustainability in food supply has led to progressive increase in soil nutrient enrichment. Fertilizer application effects both biological and abiotic processes in the soil, of which the bacterial community that support viral multiplication are equally influenced. Nevertheless, little is known on the effect of soil fertilization on the Soil viral community composition and dynamics. In this study, we evaluated the influence of soil fertilization on the maize rhizosphere viral community growing in Luvisolic soil. The highest abundance of bacteriophages were detected in soil treated with 8 tons/ha compost manure (Cp8), 60kg/ha inorganic fertilizer (N1), 4 tons/ha compost manure (Cp4) and the unfertilized control (Cn0). Our result showed higher relative abundance of Myoviridae, Podoviridae and Siphoviridae in 8 tons/ha organic manure (Cp8) fertilized compared to others. While Inoviridae and Microviridae were the most relative abundant phage families in 4 tons/ha organic manure (Cp4) fertilized soil. This demonstrate that soil fertilization with organic manure increases the abundance and diversity of viruses in the soil due to its soil conditioning effects.

Biotic and abiotic reductive dechlorination of chloroethenes in aquitards

Chlorinated solvents occur as dense nonaqueous phase liquid (DNAPL) or as solutes when dissolved in water. They are present in many pollution sites in urban and industrial areas. They are toxic, carcinogenic, and highly recalcitrant in aquifers and aquitards. In the latter case, they migrate by molecular diffusion into the matrix. When aquitards are fractured, chlorinated solvents also penetrate as a free phase through the fractures. The main objective of this study was to analyze the biogeochemical processes occurring inside the matrix surrounding fractures and in the joint-points zones. The broader implications of this objective derive from the fact that, incomplete natural degradation of contaminants in aquitards generates accumulation of daughter products. This causes steep concentration gradients and back-diffusion fluxes between aquitards and high hydraulic conductivity layers. This offers opportunities to develop remediation strategies based, for example, on the coupling of biotic and reactive abiotic processes. The main results showed: 1) Degradation occurred especially in the matrix adjacent to the orthogonal network of fractures and textural heterogeneities, where texture contrasts favored microbial development because these zones constituted ecotones. 2) A dechlorinating bacterium not belonging to the Dehalococcoides genus, namely Propionibacterium acnes, survived under the high concentrations of dissolved perchloroethene (PCE) in contact with the PCE-DNAPL and was able to degrade it to trichloroethene (TCE). Dehalococcoides genus was able to conduct PCE reductive dechlorination at least up to cis-1,2-dichloroethene (cDCE), which shows again the potential of the medium to degrade chloroethenes in aquitards. 3) Degradation of PCE in the matrix resulted from the coupling of reactive abiotic and biotic processes—in the first case, promoted by Fe2+ sorbed to iron oxides, and in the latter case, related to dechlorinating microorganisms. The dechlorination resulting from these coupling processes is slow and limited by the need for an adequate supply of electron donors.

Effect of co-existent Al(III) in As-rich Acid Mine Drainage (AMD) on As removal during Fe(II) and As(III) abiotic oxidation process

The effect of co-existent Al(III) in As-rich AMD on As removal via oxygen-induced abiotic oxidation caused concern due to weak affinity between Al(III) hydroxide and As(III). The removal of As from As-rich AMD with and without Al(III) at various pH and Fe/(Al)/As molar ratios was investigated. The results showed that 92.3–99.8% of As in Al(III)-containing systems was removed by 70–100% of Fe(II) and 40.2–67.8% of As(III) oxidation in 1–4 h at pH 3–9 and Fe/Al/As molar ratios of 2–8:1:1. Arsenic removal efficiencies generally increased with increasing the pH and Fe/Al/As molar ratio. Arsenic oxidation efficiencies first increased from pH 3 to 5 and then decreased from pH 5 to 9, while an opposite trend occurred with increasing the Fe/Al/As molar ratio. As(III) oxidation was controlled by ROS contents involving the Fenton-like reaction between Fe(II) and O2. Ferric arsenite hydroxysulfate, ferric arsenate and As-bearing ferrihydrite+schwertannite were the main As sinks. Co-existent Al(III) promoted As(III) oxidation. The proposed method for aqueous As removal with the total As (As(T)) leaching solid product at pH 5 and Fe/Al/As molar ratio of 8:1:1 can bring the As level to the required limit as emphasized in regulatory frameworks.

Influence of agro-industrial wastes over the abiotic and composting degradation of polylactic acid biocomposites

Combining polylactic acid (PLA) with waste fibers to produce reinforced biocomposites is of top interest to replace conventional polymers for environmentally friendlier materials. Natural fibers have a remarkable effect on the mechanical and thermal properties of the biocomposites. This reinforcing effect strongly depends on the chemical compositions of fibers, which will also influence the susceptibility of the biocomposites to abiotic and biotic degradation processes. This study evaluated the effect of agave and coir waste fibers over the abiotic and composting degradation of PLA-based biocomposites. Compression-molded PLA/agave and PLA/coir biocomposites using GMA-g-PLA as compatibilizer were subjected to accelerated weathering. Weathered and unweathered samples were further submitted to water absorption to analyze their hydrolytic degradation and composting for biotic degradation. Both fibers showed significant influence on biocomposites degradation. The role of the fibers in UV and hydrolytic degradation was positive for impact properties since the biocomposites were less affected than PLA. Water uptake was increased with fiber addition, while hydrolytic degradation was decreased. The weathering (abiotic degradation) accelerated the PLA biodegradation rate. In general, the results showed that adding both fibers to PLA could help its outdoor performance, maintaining the biodegradable characteristics of these materials.

Effects of sewer biofilm on the degradation of drugs in sewage: A microcosm study

A thorough understanding of the in-sewer stability of chemical biomarkers is critical in applying wastewater-based surveillance of community drug use. In this study, we examined the effects of sewer biofilm on the degradation of commonly abused drugs, namely, morphine, fentanyl, cocaine, and amphetamine, in wastewater using 48-h batch degradation tests. The experiments were designed to distinguish among abiotic, biochemical, and physical degradation processes, and used mature biofilm obtained from an actual sewer line. Parallel microcosm tests were conducted using wastewater with and without suspended biofilm. Results indicate that first order kinetics describe the degradation of the drugs in both wastewater and wastewater-biofilm microcosms. Amphetamine was most stable in all microcosms, with a maximum removal of only 34% after 48 h. Abiotic chemical transformation played a major role in the degradation of morphine (kab = 0.018 h-1), fentanyl (kab = 0.022 h-1) and cocaine (kab = 0.049 h-1) in wastewater. Fentanyl removal from wastewater was also influenced by the presence of biofilm (kf = 0.015 h-1). This study is the first to report on the effect of sewer biofilm on fentanyl degradation, and highlights the need to account for in-sewer drug stability in wastewater-based drug use estimation, particularly for chemicals with high affinity for organics.

Abiotic degradation of field wheat straw as a notable source of atmospheric carbonyls in the North China Plain

Carbonyl compounds (carbonyls) play a crucial role in atmospheric chemistry, but their atmospheric sources are not fully identified. Here we show unexpectedly high carbonyl emissions from extensive field returning wheat straw over the North China Plain (NCP). The emission rates of carbonyls exhibit distinct diurnal variations with the noontime peak value of total carbonyls greater than 135 μg∙kg−1 (dry straw weight) ∙h−1. The carbonyl emission is mainly attributed to biomass abiotic degradation processes that are affected by air temperature and sunlight intensity. Given that the photolysis of carbonyls is the major primary source of ROx radicals in the troposphere, carbonyl emissions would lead to increasing atmospheric oxidants. The mean daytime O3 concentration over the NCP increases by 12.3% when coupling carbonyl emissions from wheat straw with the current emission inventory through the model simulation. It might be one of the important reasons for the occurrence of the most serious O3 pollution in June when winter wheat is intensively harvested in the region. Further studies are warranted to explore the influence of field returning wheat straw on regional air quality.

Dissolved iron cycling in the Arabian Sea and sub-tropical gyre region of the Indian Ocean

Understanding the sources and biogeochemical processes influencing the dissolved iron (DFe) distribution is crucial because of its coupled role in C- and N-fixation in the oceans. Vertical depth profiles of DFe in the northwestern Indian Ocean along two meridional transects (∼65 °E and ∼57 °E) during spring and fall seasons are presented here under the GEOTRACES-INDIA initiative. The DFe in the surface waters exhibited both spatial and seasonal variabilities; N-S gradient with higher values in the north; and notably higher concentrations in the fall season. The photic zone-integrated DFe (57.5 ± 13.4 µmol m−2) was double in the Arabian Sea compared to the subtropical Indian Ocean (31.81 ± 7.63 µmol m−2) with a significant positive correlation with the photic zone integrated primary production. This suggests higher availability of DFe is responsible for high primary production in the Arabian Sea compared to the subtropical Indian Ocean. Lateral and vertical advection along with particle dissolution from the atmospheric dust fluxes and scavenging-adsorption processes could play prominent role in controlling photic DFe concentrations in the Arabian Sea. The continental margin sources, redox chemistry, and remineralization are responsible for the observed high DFe concentration within the intense oxygen minimum zone. The in-situ remineralization ratios of Fe to C in the Arabian Sea are higher than any other region of the Indian Ocean. It could be due to the high uptake of Fe during primary production in the Arabian Sea, despite huge spatio-temporal variations in the abundance of phytoplankton communities. Our DFe data from the undersampled region over the Carlsberg Ridge suggests the presence of chronic/event plumes contributing to the DFe inventory in the western Arabian Sea region.We have approximated the geochemical budget of Fe in the top 100 m for open ocean waters of the Arabian Sea. These preliminary estimates suggest that lateral and vertical fluxes for DFe are prominent in the region compared to soluble atmospheric Fe dust fluxes and these sources are balanced by the biotic and abiotic removal processes in the region. Based on these estimated fluxes, the calculated residence time of DFe varies from ∼0.1 to 1 year in photic waters of the Arabian Sea. Our results highlight the intrusion of Fe-deficit Southern Ocean waters in the Arabian Sea and the upwelling of Fe-starved deep waters alongside the northwest of the Murray Ridge are likely responsible for Fe limitation in the region.

Post-depositional modification of carbonate ooids by sulfate-reducing bacteria: Evidence from the Lower–Middle Jurassic, Tethyan Himalayas of southern Tibet

The role of microbial vs. abiotic processes in ooid formation has been a controversial topic for over a century. Recent sedimentological, geochemical and biomarker data indicate that microbes make an important contribution to the construction, destruction and modification of ooids. Here, we present a detailed petrographic and chemical investigation of well-preserved red oolites from the Lower–Middle Jurassic Nieniexiongla Formation in the Tethyan Himalaya of southern Tibet. Petrographic studies and electron probe microanalysis indicate that the red coloration is due to the presence of hematite minerals. The hematites show euhedral and amorphous spheroidal morphology and residual elemental sulfur was detected within minerals. The δ34S values in the leachate (δ34SNaCl) and in carbonate associated sulfate (δ34SCAS) of red oolites are lower than gray oolites and micritic limestones. Moreover, δ34SNaCl and δ34SCAS values are lowest in samples with the highest content of hematitic ooids. Together, these observations suggest that the hematites are transformed from pyrite. The Fe2+ (and possibly SO42−) provided by pore-water combined with degradation of syn-depositional organic matter within ooids produced anoxic microenvironments that facilitated local pyrite precipitation. Some spheroidal pyrites were subsequently transformed to euhedral crystals through continuous growth of the constituent microcrystals. This study demonstrates that organomineralization mediated by sulfate-reducing bacteria can produce pyrite grains within carbonate ooids. The results emphasize the important role that microbial communities play in the deposition and modifications of ooids.

Biogenic formation of amorphous carbon by anaerobic methanotrophs and select methanogens.

Elemental carbon exists in different structural forms including graphite, diamond, fullerenes, and amorphous carbon. In nature, these materials are produced through abiotic chemical processes under high temperature and pressure but are considered generally inaccessible to biochemical synthesis or breakdown. Here, we identified and characterized elemental carbon isolated from consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB), which together carry out the anaerobic oxidation of methane (AOM). Two different AOM consortia, ANME-1a/HotSeep-1 and ANME-2a/c/Seep-SRB, produce a black material with similar characteristics to disordered graphite and amorphous carbon. Stable isotope probing studies revealed that the carbon is microbially generated during AOM. In addition, we found that select methanogens also produce amorphous carbon with similar characteristics to the carbon from AOM consortia. Biogenic amorphous carbon may serve as a conductive element to facilitate electron transfer, or redox active functional groups associated with the carbon could act as electron donors and acceptors.

Melatonin Confers Plant Cadmium Tolerance: An Update.

Cadmium (Cd) is one of the most injurious heavy metals, affecting plant growth and development. Melatonin (N-acetyl-5-methoxytryptamine) was discovered in plants in 1995, and it is since known to act as a multifunctional molecule to alleviate abiotic and biotic stresses, especially Cd stress. Endogenously triggered or exogenously applied melatonin re-establishes the redox homeostasis by the improvement of the antioxidant defense system. It can also affect the Cd transportation and sequestration by regulating the transcripts of genes related to the major metal transport system, as well as the increase in glutathione (GSH) and phytochelatins (PCs). Melatonin activates several downstream signals, such as nitric oxide (NO), hydrogen peroxide (H2O2), and salicylic acid (SA), which are required for plant Cd tolerance. Similar to the physiological functions of NO, hydrogen sulfide (H2S) is also involved in the abiotic stress-related processes in plants. Moreover, exogenous melatonin induces H2S generation in plants under salinity or heat stress. However, the involvement of H2S action in melatonin-induced Cd tolerance is still largely unknown. In this review, we summarize the progresses in various physiological and molecular mechanisms regulated by melatonin in plants under Cd stress. The complex interactions between melatonin and H2S in acquisition of Cd stress tolerance are also discussed.

Multi-element isotopic evidence for monochlorobenzene and benzene degradation under anaerobic conditions in contaminated sediments

Industrial chemicals are frequently detected in sediments due to a legacy of chemical spills. Globally, site remedies for groundwater and sediment decontamination include natural attenuation by in situ abiotic and biotic processes. Compound-specific isotope analysis (CSIA) is a diagnostic tool to identify, quantify, and characterize degradation processes in situ, and in some cases can differentiate between abiotic degradation and biodegradation. This study reports high-resolution carbon, chlorine, and hydrogen stable isotope profiles for monochlorobenzene (MCB), and carbon and hydrogen stable isotope profiles for benzene, coupled with measurements of pore water concentrations in contaminated sediments. Multi-element isotopic analysis of δ13C and δ37Cl for MCB were used to generate dual-isotope plots, which for 2 locations at the study site resulted in ΛC/Cl(130) values of 1.42 ± 0.19 and ΛC/Cl(131) values of 1.70 ± 0.15, consistent with theoretical calculations for carbon-chlorine bond cleavage (ΛT = 1.80 ± 0.31) via microbial reductive dechlorination. For benzene, significant δ2H (122‰) and δ13C (6‰) depletion trends, followed by enrichment trends in δ13C (1.6‰) in the upper part of the sediment, were observed at the same location, indicating not only production of benzene due to biodegradation of MCB, but subsequent biotransformation of benzene itself to nontoxic end-products. Degradation rate constants calculated independently using chlorine isotopic data and carbon isotopic data, respectively, agreed within uncertainty thus providing multiple lines of evidence for in situ contaminant degradation via reductive dechlorination and providing the foundation for a novel approach to determine site-specific in situ rate estimates essential for the prediction of remediation outcomes and timelines.

Transcriptome-Wide Analysis and Functional Verification of RING-Type Ubiquitin Ligase Involved in Tea Plant Stress Resistance.

The ubiquitin/26S proteasome pathway is a critical protein-degradation pathway in plant growth and development as well as in nearly all biological and abiotic stress processes. Although as a member of the ubiquitin/26S proteasome pathway, the E3 ubiquitin ligase family has been shown to be essential for the selective degradation of downstream target proteins, it has been rarely reported in tea plants (Camellia sinensis). In this study, through database searches and extensive manual deduplication, 335 RING finger family proteins were selected from the Tea Plant Information Archive. These proteins were divided into six categories by the difference of RING finger domain: RING-H2, RING-HCa, RING-HCb, RING-C2, RING-v, and RING-G. Stress-induced differential gene expression analysis showed that 53 proteins in RING finger family can respond to selected exogenous stress. In vitro ubiquitination assays indicated that TEA031033, which was named CsMIEL1, exhibited the activity of E3 ubiquitin ligases. CsMIEL1-overexpressing transgenic Arabidopsis thaliana seedlings were resistant to some exogenous abiotic stresses, such as salt and drought stress but sensitive to exogenous methyl jasmonate treatment. Furthermore, CsMIEL1 reduced the accumulation of anthocyanin in transgenic plants in response to low temperature treatment. The results of this article provide basic date for studying the role of ubiquitin/26S proteasome pathway in tea plants response to stresses.

Litter inputs and phosphatase activity affect the temporal variability of organic phosphorus in a tropical forest soil in the Central Amazon

PurposeThe tropical phosphorus cycle and its relation to soil phosphorus (P) availability are a major uncertainty in projections of forest productivity. In highly weathered soils with low P concentrations, plant and microbial communities depend on abiotic and biotic processes to acquire P. We explored the seasonality and relative importance of drivers controlling the fluctuation of common P pools via processes such as litter production and decomposition, and soil phosphatase activity.MethodsWe analyzed intra-annual variation of tropical soil phosphorus pools using a modified Hedley sequential fractionation scheme. In addition, we measured litterfall, the mobilization of P from litter and soil extracellular phosphatase enzyme activity and tested their relation to fluctuations in P- fractions.ResultsOur results showed clear patterns of seasonal variability of soil P fractions during the year. We found that modeled P released during litter decomposition was positively related to change in organic P fractions, while net change in organic P fractions was negatively related to phosphatase activities in the top 5 cm.ConclusionWe conclude that input of P by litter decomposition and potential soil extracellular phosphatase activity are the two main factors related to seasonal soil P fluctuations, and therefore the P economy in P impoverished soils. Organic soil P followed a clear seasonal pattern, indicating tight cycling of the nutrient, while reinforcing the importance of studying soil P as an integrated dynamic system in a tropical forest context.

Fine-Scale Spatial Structure of Soil Microbial Communities in Burrows of a Keystone Rodent Following Mass Mortality

Soil microbial communities both reflect and influence biotic and abiotic processes occurring at or near the soil surface. Ecosystem engineers that physically alter the soil surface, such as burrowing ground squirrels, are expected to influence the distribution of soil microbial communities. Black-tailed prairie dogs (Cynomys ludovicianus) construct complex burrows in which activities such as nesting, defecating, and dying are partitioned spatially into different chambers. Prairie dogs also experience large-scale die-offs due to sylvatic plague, caused by the bacterium Yersinia pestis, which lead to mass mortality events with potential repercussions on microbial communities. We used 16S sequencing to examine microbial communities in soil that was excavated by prairie dogs from different burrow locations, and surface soil that was used in the construction of burrow entrances, in populations that experienced plague die-offs. Following the QIIME2 pipeline, we assessed microbial diversity at several taxonomic levels among burrow regions. To do so, we computed community similarity metrics (Bray–Curtis, Jaccard, and weighted and unweighted UniFrac) among samples and community diversity indexes (Shannon and Faith phylogenetic diversity indexes) within each sample. Microbial communities differed across burrow regions, and several taxa exhibited spatial variation in relative abundance. Microbial ecological diversity (Shannon index) was highest in soil recently excavated from within burrows and soils associated with dead animals, and was lowest in soils associated with scat. Phylogenetic diversity varied only marginally within burrows, but the trends paralleled those for Shannon diversity. Yersinia was detected in four samples from one colony, marking the first time the genus has been sampled from soil on prairie dog colonies. The presence of Yersinia was a significant predictor of five bacterial families and eight microbial genera, most of which were rare taxa found in higher abundance in the presence of Yersinia, and one of which, Dictyostelium, has been proposed as an enzootic reservoir of Y. pestis. This study demonstrates that mammalian modifications to soil structure by physical alterations and by mass mortality can influence the distribution and diversity of microbial communities.