Shifts In Microbial Community Structure Research Articles

Unraveling Nitrogen, Sulfur, and Carbon Metabolic Pathways and Microbial Community Transcriptional Responses to Substrate Deprivation and Toxicity Stresses in a Bioreactor Mimicking Anoxic Brackish Coastal Sediment Conditions

Microbial communities are key drivers of carbon, sulfur, and nitrogen cycling in coastal ecosystems, where they are subjected to dynamic shifts in substrate availability and exposure to toxic compounds. However, how these shifts affect microbial interactions and function is poorly understood. Unraveling such microbial community responses is key to understand their environmental distribution and resilience under current and future disturbances. Here, we used metagenomics and metatranscriptomics to investigate microbial community structure and transcriptional responses to prolonged ammonium deprivation, and sulfide and nitric oxide toxicity stresses in a controlled bioreactor system mimicking coastal sediment conditions. Ca. Nitrobium versatile, identified in this study as a sulfide-oxidizing denitrifier, became a rare community member upon ammonium removal. The ANaerobic Methanotroph (ANME) Ca. Methanoperedens nitroreducens showed remarkable resilience to both experimental conditions, dominating transcriptional activity of dissimilatory nitrate reduction to ammonium (DNRA). During the ammonium removal experiment, increased DNRA was unable to sustain anaerobic ammonium oxidation (anammox) activity. After ammonium was reintroduced, a novel anaerobic bacterial methanotroph species that we have named Ca. Methylomirabilis tolerans outcompeted Ca. Methylomirabilis lanthanidiphila, while the anammox Ca. Kuenenia stuttgartiensis outcompeted Ca. Scalindua rubra. At the end of the sulfide and nitric oxide experiment, a gammaproteobacterium affiliated to the family Thiohalobacteraceae was enriched and dominated transcriptional activity of sulfide:quinone oxidoreductases. Our results indicate that some community members could be more resilient to the tested experimental conditions than others, and that some community functions such as methane and sulfur oxidation coupled to denitrification can remain stable despite large shifts in microbial community structure. Further studies on complex bioreactor enrichments are required to elucidate coastal ecosystem responses to future disturbances.

Two Metatranscriptomic Profiles through Low-Dissolved-Oxygen Waters (DO, 0 to 33 µM) in the Eastern Tropical North Pacific Ocean.

ABSTRACTWe present 16 seawater metatranscriptomes collected from a marine oxygen-deficient zone (ODZ) in the eastern tropical North Pacific (ETNP). This data set will be useful for identifying shifts in microbial community structure and function through oxic/anoxic transition zones, where overlapping aerobic and anaerobic microbial processes impact marine biogeochemical cycling.

Shifts in microbial community structure and function in polycyclic aromatic hydrocarbon contaminated soils at petrochemical landfill sites revealed by metagenomics

Investigations of the microbial community structures, potential functions and polycyclic aromatic hydrocarbon (PAH) degradation-related genes in PAH-polluted soils are useful for risk assessments, microbial monitoring, and the potential bioremediation of soils polluted by PAHs. In this study, five soil sampling sites were selected at a petrochemical landfill in Beijing, China, to analyze the contamination characteristics of PAHs and their impact on microorganisms. The concentrations of 16 PAHs were detected by gas chromatography-mass spectrometry. The total concentrations of the PAHs ranged from ND to 3166.52 μg/kg, while phenanthrene, pyrene, fluoranthene and benzo [ghi]perylene were the main components in the soil samples. According to the specific PAH ratios, the PAHs mostly originated from petrochemical wastes in the landfill. The levels of the total toxic benzo [a]pyrene equivalent (1.63–107.73 μg/kg) suggested that PAHs might result in adverse effects on soil ecosystems. The metagenomic analysis showed that the most abundant phyla in the soils were Proteobacteria and Actinobacteria, and Solirubrobacter was the most important genus. At the genus level, Bradyrhizobium, Mycobacterium and Anaeromyxobacter significantly increased under PAH stress. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations, the most abundant category of functions that are involved in adapting to contaminant pressures was identified. Ten PAH degradation-related genes were significantly influenced by PAH pressure and showed correlations with PAH concentrations. All of the results suggested that the PAHs from the petrochemical landfill could be harmful to soil environments and impact the soil microbial community structures, while microorganisms would change their physiological functions to resist pollutant stress.

Alkaline mine drainage drives stream sediment microbial community structure and function

With advances in eDNA metabarcoding, environmental microbiomes are increasingly used as cost-effective tools for monitoring ecosystem health. Stream ecosystems in Central Appalachia, heavily impacted by alkaline drainage from mountaintop coal mining, present ideal opportunities for biomonitoring using stream microbiomes, but the structural and functional responses of microbial communities in different environmental compartments are not well understood. We investigated sediment microbiomes in mining impacted streams to determine how community composition and function respond to mining and to look for potential microbial bioindicators. Using 16s rRNA gene amplicon sequencing, we found that mining leads to shifts in microbial community structure, with the phylum Planctomycetes enriched by 1-6% at mined sites. We observed ~51% increase in species richness in bulk sediments. In contrast, of the 31 predicted metabolic pathways that changed significantly with mining, 23 responded negatively. Mining explained 15-18% of the variance in community structure and S, Se, %C and %N were the main drivers of community and functional pathway composition. We identified 12 microbial indicators prevalent in the ecosystem and sensitive to mining. Overall, alkaline mountaintop mining drainage causes a restructuration of the sediment microbiome, and our study identified promising microbial indicators for the long-term monitoring of these impacted streams.

Biochar amendment rapidly shifts microbial community structure with enhanced thermophilic digestion activity

Effects of powdered (<0.075 mm) biochar on thermophilic anaerobic digestion were investigated with biochemical methane potential (BMP) assays. The assays had substrate to inoculum ratios (SIR) of 2.2 and 4.4 g-volatile solids (VS)/g-VS and biochar dosing of 6 g/g-total solids (TS)inoculum. Compared to control, biochar amendment enhanced methane production rates by 94%, 75%, and 20% in assays utilizing substrates of acidified sludge at 70 °C, 55 °C and non-acidified mixed sludge, respectively. All controls experienced acute inhibition with lag phases from 12 − 52 days at SIR of 4.4 g-VS/g-VS, while assays with biochar generated methane from day 4. Biochar addition resulted in a rapid shift in microbial community structure associated with an increase in Methanothermobacteraeae (hydrogenotrophic) and Methanosarcinaceae archaea, as well as various volatile fatty acid (VFA)-degrading and hydrogen-producing bacteria. Biochar presents great potential to tackle VFA accumulation, abbreviate lag phase and increase methane rate, particularly at high organic loadings.

Limited resilience of the soil microbiome to mechanical compaction within four growing seasons of agricultural management

Soil compaction affects many soil functions, but we have little information on the resistance and resilience of soil microorganisms to this disturbance. Here, we present data on the response of soil microbial diversity to a single compaction event and its temporal evolution under different agricultural management systems during four growing seasons. Crop yield was reduced (up to −90%) in the first two seasons after compaction, but mostly recovered in subsequent seasons. Soil compaction increased soil bulk density (+15%), and decreased air permeability (−94%) and gas diffusion (−59%), and those properties did not fully recover within four growing seasons. Soil compaction induced cropping system-dependent shifts in microbial community structures with little resilience over the four growing seasons. Microbial taxa sensitive to soil compaction were detected in all major phyla. Overall, anaerobic prokaryotes and saprotrophic fungi increased in compacted soils, whereas aerobic prokaryotes and plant-associated fungi were mostly negatively affected. Most measured properties showed large spatial variability across the replicated blocks, demonstrating the dependence of compaction effects on initial conditions. This study demonstrates that soil compaction is a disturbance that can have long-lasting effects on soil properties and soil microorganisms, but those effects are not necessarily aligned with changes in crop yield.

Microbial Community Structure and Diversity in Drinking Water Supply, Distribution Systems as well as Household Point of Use Sites in Addis Ababa City, Ethiopia.

Understanding ecology of microbiomes in drinking water distribution systems is the most important notion in delivering safe drinking water. Drinking water distribution systems harbor various microbiota despite efforts made in improving water infrastructures in the water industry, especially, in developing countries. Intermittent water supply, long time of water storage, low water pressure, and contaminated source water are among many of the factors responsible for poor drinking water quality affecting health of people. The aim of this study was to explore microbial diversity and structure in water samples collected from source water, treated water, reservoirs, and household points of use locations (taps). High-throughput Illumina sequencing technology was employed by targeting the V4 region of the 16S rRNA gene and the V1-V3 region of the 18S rRNA gene to analyze the microbial community structure. Proteobacteria followed by Firmicutes, Bacteroidetes, and Actinobacteria were the core dominating taxa. Gammaproteobacteria was also dominant among other proteobacterial classes across all sampling points. Opportunistic bacterial genera such as Pseudomonas, Legionella, Klebsiella, Escherichia, and Actinobacteria, as well as eukaryotic microbes like Cryptosporidium, Hartmannella, Acanthamoeba, Aspergillus, and Candida were also abundant taxa found along the distribution systems. The shift in microbial community structure from source to point of use locations was influenced by basic factors such as residual chlorine, intermittent water supply, and long-time storage at the household. The complex microbiota detected in different sampling sites in this study brings drinking water quality problem which further causes significant health problems to both human and animal health. Treatment ineffectiveness, disinfection inefficiency, poor maintenance actions, leakage of sewage, and other domestic wastes are few among many other factors responsible for degraded drinking water quality in this study putting health at high risk. Findings of this research provide important and baseline information to understand the microbial profiles of drinking water along source water and distribution systems. Moreover, knowing the microbial profile will help to design proper water quality assurance approaches.

Responses of cucumber (Cucumis sativus L.) rhizosphere microbial community to some agronomic management practices.

The microbial communities associated to the rhizosphere (the rhizomicrobiome) have a substantial impact on plant growth and yield. Understanding the effects of agricultural management on the rhizomicrobiome is very important for selecting efficient practices. By sequencing the V4 region of 16S rRNA for bacteria and the ITS1 regions and fungi, we investigated the influences of agronomic practices, including cucumber grafting on cucurbit hybrid (Cucurbita moschata × C. maxima), cucumber-garlic intercropping, and treatment with fungicide iprodione-carbendazim on cucumber rhizosphere microbial communities during plant growth. Soil dehydrogenase activity (DHA) and plant vegetative parameters were assessed as an indicator of overall soil microbial activity. We found that both treatments and growth stage induced significant shifts in microbial community structure. Grafting had the highest number of differentially abundant OTUs compared to control samples, followed by intercropping and fungicide treatment, while plant development stage affected both alpha and beta diversities indices and composition of the rhizomicrobiome. DHA was more dependent on plant growth stages than on treatments. Among the assessed factors, grafting and plant developmental stage resulted in the greatest changes in the microbial community composition. Grafting also increased the plant growth parameters, suggesting that this method should be further investigated in vegetable production systems.

Coeval Drying Across the Central Tropical Pacific Over the Last Millennium

AbstractHydroclimatic variability in the tropical Pacific reflects large‐scale ocean‐atmosphere processes that imprint on global climate, but tropical Pacific hydroclimate variability over the last millennium remains uncertain. Here we present a multi‐proxy reconstruction from a lacustrine sediment record on Kiritimati Atoll that spans the last millennium. A lake salinity reconstruction from the δ2H values of total lipid extracts, combined with changes in sediment mineralogy and the stable isotopic composition of inorganic carbonates, indicate the presence of several distinct hydrologic regimes on Kiritimati, including a period of persistent aridity from 960–1030 CE, shorter episodes of aridity from 1030–1370 CE, and extreme aridity throughout the latter half of the last millennium, from 1370–1970 CE, that drove complete evaporation of the lake. A period of wetter, variable conditions defines recent decades. Compound‐specific lipid biomarker δ2H values indicate that shifts in microbial community structure occurred in the past, from a community dominated by photoautotrophic and chemoautotrophic organisms in more arid periods to a more metabolically diverse community in the recent period. Comparison of this record with nearby sediment records from Washington Island reveals a similar pattern of aridity through the last millennium, followed by wetter conditions in the modern period. These coherent changes in hydroclimate in the central Pacific are inconsistent with a migration of the Pacific Intertropical Convergence Zone within these latitudes. Rather, past aridity was caused by reduced El Niño‐Southern Oscillation variability, observed through the low‐pass filter of lacustrine records, or by multidecadal to multi‐century strengthening of the Pacific Walker Circulation.

Uncertainty quantification of the soil moisture response functions for microbial dormancy and resuscitation

Abiotic factors influence ecosystem functioning mainly through the biological mechanisms such as the shifts in microbial community structure and/or physiology. Sigmoidal shape soil moisture response functions (SMRFs) have been widely used to modify the dormancy and resuscitation rates in microbially explicit soil biogeochemical models. However, these SMRFs and their effects on microbial dormancy have not been well quantified with experimental data. Using observations from a three-year field experiment in subtropical forests, we conducted a comprehensive parameterization of typical sigmoidal SMRFs. We quantified uncertainties in the three parameters of these SMRFs: (i) the critical soil water potential (SWP) for microbes entering dormancy, φA2D=−0.46±0.03MPa (mean ± standard deviation); (ii) the ratio of the critical SWP for resuscitation to φA2D, τ=0.39±0.16; and (iii) the exponent in the SMRFs, ω=3.38±0.54. Our results show much higher uncertainty in the SMRF for microbial resuscitation than microbial dormancy, due to the parameter τ being included in microbial reactivation with larger uncertainty than that of φA2D and ω. In addition, the active microbes, rather than the total living microbes, were overwhelmingly controlled by soil moisture, leading to the stronger dependency of microbial respiration on soil moisture in the dry season than in the wet season. The SMRFs and their parameter values/uncertainties derived in this study could be directly incorporated into or used as a priori in ecosystem and Earth system models that account for microbial dormancy and resuscitation.

Magnesium and nitrogen drive soil bacterial community structure under long-term apple orchard cultivation systems

Apple replant disease (ARD) is a common and destructive disease in apple orchards with long cultivation histories. In the present study, soils from three apple orchards under cultivation for two years (G2), thirty years (G30), and forty years (G40) were used to investigate the key nutritional factors influencing soil bacterial community structure. Changes in nutrient concentrations in the orchard soil entailed reductions in concentrations of medium trace nutrients (magnesium [Mg], manganese, and nickel) and the increase in concentrations of macronutrients (total nitrogen [TN], total phosphorus, total potassium, available phosphorus, and available potassium) and soil organic carbon. As cultivation time was prolonged, bacterial community composition shifted from enrichment with oligotrophic Acidobacteria and plant growth-facilitated Streptomyces to increased abundance of copiotrophic taxa, Bacteroidetes and Firmicutes, and plant-growth-impairing Gemmatimonas, based on 16S rDNA (V4) amplicon sequencing data. In addition, the relative abundances of bacteria associated with fermentation function and the decomposition of some unique compound classes increased, while the relative abundance of bacteria associated with the nitrification function decreased. Among all the nutritional elements tested using distance-based multivariate linear model analysis, Mg and TN influenced community structure the most. The results provide novel insights into the associations between soil nutrients and shifts in microbial community structure under long-term apple orchard soil ecosystems.

Impact of diesel and biodiesel contamination on soil microbial community activity and structure

Soil contamination as a result of oil spills is a serious issue due to the global demand for diesel fuel. As an alternative to diesel, biodiesel has been introduced based on its high degradability rates and potential for reducing of greenhouse gases emissions. This study assessed the impacts diesel and biodiesel contamination on soil microbial community activity and structure. Our results suggest higher microbial activity in biodiesel contaminated soils and analysis of PLFA profiles confirmed shifts in microbial community structure in response to contamination. High-throughput 16S rRNA amplicon sequencing also revealed a lower bacterial richness and diversity in contaminated soils when compared to control samples, supporting evidence of the detrimental effects of hydrocarbons on soil microbiota. Control samples comprised mostly of Actinobacteria, whereas Proteobacteria were predominantly observed in diesel and biodiesel contaminated soils. At genus level, diesel and biodiesel amendments highly selected for Rhodococcus and Pseudomonas spp., respectively. Moreover, predicted functional profiles based on hydrocarbon-degrading enzymes revealed significant differences between contaminated soils mostly due to the chemical composition of diesel and biodiesel fuel. Here, we also identified that Burkholderiaceae, Novosphingobium, Anaeromyxobacter, Pseudomonas and Rhodococcus were the main bacterial taxa contributing to these enzymes. Together, this study supports the evidence of diesel/biodiesel adverse effects in soil microbial community structure and highlights microbial taxa that could be further investigated for their biodegradation potential.

Recurrent microbial community types driven by nearshore and seasonal processes in coastal Southern California.

A multitude of concurrent biological and physical processes contribute to microbial community turnover, especially in highly dynamic coastal environments. Characterizing what factors contribute most to shifts in microbial community structure and the specific organisms that correlate with changes in the products of photosynthesis improves our understanding of nearshore microbial ecosystem functions. We conducted high frequency sampling in nearshore Southern California in order to capture sub-weekly microbial community dynamics. Microbial communities were characterized by flow cytometry and 16S rRNA gene sequencing, and placed in the context of physicochemical parameters. Within our time-series, season and nutrient availability corresponded to changes in dominant microbial community members. Concurrent aseasonal drivers with overlapping scales of variability were also apparent when we used network analysis to assess the microbial community as subsets of the whole. Our analyses revealed the microbial community as a mosaic, with overlapping groups of taxa that varied on different timescales and correlated with unique abiotic and biotic factors. Specifically, a subnetwork associated with chlorophyll a exhibited rapid turnover, indicating that ecologically important subsets of the microbial community can change on timescales different than and in response to factors other than those that govern turnover of most members of the assemblage.

Microbial community structure shifts and potential Symbiodinium partner bacterial groups of bleaching coral Pocillopora verrucosa in South China Sea.

The community structure of coral associated microorganisms will change greatly in coral bleaching. However, the relationship between specific bacteria groups and Symbiodinium, which is easy to be found in the bleaching process, has been ignored for a long time. In this study, the changes of coral microbial community during a natural bleaching event in the South China Sea were studied by 16S rRNA gene high-throughput sequencing. The microbial community composition of bleached corals was significantly different from that of normal corals (P < 0.001). OTUs belong to Bacillus, Exiguobacterium, Oceanobacillus, Saccharibacteria and Ostreobiaceae was significantly increased in the bleaching corals. The relative abundance of 30.9% OTUS changed significantly during coral bleaching. The relative abundance of potential coral pathogenic groups was not significantly different between normal and bleaching corals. Symbiodinium positively correlated bacterial groups accounted for 6.9% and 4.3% in the normal corals and bleached corals, respectively. The dominated groups of potential Symbiodinium-partner bacteria are Lactococcus and Bacillus. The potential Symbiodinium-partner bacterial groups in bleached corals were significantly lower than that in the normal corals, which further showed their coexistence with Symbiodinium. This study provides insight into the role of potential Symbiodinium-partner bacterial groups in the coral bleaching process and supports the theory of beneficial microorganisms for corals.

Raw Milk-Induced Protection against Food Allergic Symptoms in Mice Is Accompanied by Shifts in Microbial Community Structure.

The mechanism underlying the allergy-protective effects of raw cow’s milk is still unknown, but the modulation of the gut microbiome may play a role. The effects of consuming raw cow’s milk or processed milk on fecal microbial communities were therefore characterized in an experimental murine model. C3H/HeOuJ mice were treated with raw milk, pasteurized milk, skimmed raw milk, pasteurized milk supplemented with alkaline phosphatase (ALP), or phosphate-buffered saline (PBS) for eight days prior to sensitization and challenge with ovalbumin (OVA). Fecal samples were collected after milk exposure and after OVA sensitization, and microbiomes were characterized using 16S ribosomal RNA gene amplicon sequencing. Treatment with raw milk prior to OVA sensitization increased the relative abundance of putative butyrate-producing bacteria from the taxa Lachnospiraceae UCG-001, Lachnospiraceae UCG-008, and Ruminiclostridium 5 (Clostridial clusters XIVa and IV), while it decreased the relative abundance of Proteobacterial genera such as Parasutterella, a putative pro-inflammatory bacterial genus. This effect was observed after eight days of raw milk exposure and became more pronounced five weeks later, after allergic sensitization in the absence of milk. Similar trends were observed after treatment with skimmed raw milk. Conversely, the feeding of pasteurized milk led to a loss of allergy protection and a putative dysbiotic microbiome. The addition of ALP to pasteurized milk restored the protective effect observed with raw milk and mitigated some of the microbial community alterations associated with milk pasteurization. Raw milk-induced protection against food allergic symptoms in mice is accompanied by an increased relative abundance of putative butyrate-producing Clostridiales and a decreased relative abundance of putative pro-inflammatory Proteobacteria. Given the safety concerns regarding raw milk consumption, this knowledge is key for the development of new, microbiologically safe, preventive strategies to reduce the incidence of allergic diseases.

Microbial dynamics associated with the decomposition of coconut and maize residues in a microcosm experiment with tropical soils under two nitrogen fertilization levels.

The microbial dynamics associated with the decomposition of maize (Zea mays) and coconut (Cocos nucifera) residues were investigated to assess the feasibility of using them as mulch in tropical soils. Phospholipid fatty-acid (PLFA) profiling, microbial biomass (MB-C), basal respiration, C-cycle enzyme activities and inorganic N dynamics were monitored in a microcosm experiment incubating soil samples with plant residues for 425days. Maize stover (MS) showed a higher decomposition, respiration rate, MB-C, enzymes activities and shift in microbial community structure than coconut husk (CH), which was barely changed. In MS, the lower N level increased C losses and decreased N mineralization compared to the higher N level. Maize stover is suitable for mulching and has a high potential of increasing soil quality if the proper N fertilization level is used, avoiding excessive C mineralization and N immobilization. Coconut husk decomposition was mostly impaired, indicating that a pre-processing is necessary to improve the benefits of this residue. Tropical soils are prone to degradation. Mulching can promote soil conservation, but depends on residue type and soil chemistry. Our study showed that MS managed under the recommended N fertilization level is suitable for mulching while CH is highly inaccessible for microbial degradation.

Patterns in Benthic Microbial Community Structure Across Environmental Gradients in the Beaufort Sea Shelf and Slope.

The paradigm of tight pelagic-benthic coupling in the Arctic suggests that current and future fluctuations in sea ice, primary production, and riverine input resulting from global climate change will have major impacts on benthic ecosystems. To understand how these changes will affect benthic ecosystem function, we must characterize diversity, spatial distribution, and community composition for all faunal components. Bacteria and archaea link the biotic and abiotic realms, playing important roles in organic matter (OM) decomposition, biogeochemical cycling, and contaminant degradation, yet sediment microbial communities have rarely been examined in the North American Arctic. Shifts in microbial community structure and composition occur with shifts in OM inputs and contaminant exposure, with implications for shifts in ecological function. Furthermore, the characterization of benthic microbial communities provides a foundation from which to build focused experimental research. We assessed diversity and community structure of benthic prokaryotes in the upper 1 cm of sediments in the southern Beaufort Sea (United States and Canada), and investigated environmental correlates of prokaryotic community structure over a broad spatial scale (spanning 1,229 km) at depths ranging from 17 to 1,200 m. Based on hierarchical clustering, we identified four prokaryotic assemblages from the 85 samples analyzed. Two were largely delineated by the markedly different environmental conditions in shallow shelf vs. upper continental slope sediments. A third assemblage was mainly comprised of operational taxonomic units (OTUs) shared between the shallow shelf and upper slope assemblages. The fourth assemblage corresponded to sediments receiving heavier OM loading, likely resulting in a shallower anoxic layer. These sites may also harbor microbial mats and/or methane seeps. Substructure within these assemblages generally reflected turnover along a longitudinal gradient, which may be related to the quantity and composition of OM deposited to the seafloor; bathymetry and the Mackenzie River were the two major factors influencing prokaryote distribution on this scale. In a broader geographical context, differences in prokaryotic community structure between the Beaufort Sea and Norwegian Arctic suggest that benthic microbes may reflect regional differences in the hydrography, biogeochemistry, and bathymetry of Arctic shelf systems.

Root exudates increase soil respiration and alter microbial community structure in alpine permafrost and active layer soils

Due to climate warming, alpine ecosystems are changing rapidly. Ongoing upward migrations of plants and thus an increase of easily decomposable substrates will strongly affect the soil microbiome. To understand how belowground communities will respond to such changes, we set up an incubation experiment with permafrost and active soil layers from northern (NW) and southern (SE) slopes of a mountain ridge on Muot da Barba Peider in the Swiss Alps and incubated them with or without artificial root exudates (AREs) at two temperatures, 4°C or 15°C. The addition of AREs resulted in elevated respiration across all soil types. Bacterial and fungal alpha diversity decreased significantly, coinciding with strong shifts in microbial community structure in ARE-treated soils. These shifts in bacterial community structure were driven by an increased abundance of fast-growing copiotrophic taxa. Fungal communities were predominantly affected by AREs in SE active layer soils and shifted towards fast-growing opportunistic yeast. In contrast, in the colder NW facing active layer and permafrost soils fungal communities were more influenced by temperature changes. These findings demonstrate the sensitivity of soil microbial communities in high alpine ecosystems to climate change and how shifts in these communities may lead to functional changes impacting biogeochemical processes.

Deciphering microplastic ecotoxicology: impacts on crops and soil ecosystem functions

Review on microplastic toxicity in agroecosystems is scarce. Thus, we develop a conceptual model (based on literature to date) that describes various microplastic effects using a size-scale. We also classify crops depending on their observed responses, and discuss several conceptual mechanisms of soil functions. The model shows that microplastic effects on crops can be positive, toxic, lethal and no-effect. Predominantly, microfibers in a wide range of sizes can positively affect crops. However, toxic effects of microplastics with/without other pollutants are more common at different sizes. Surprisingly, biodegradable plastic effects are lethal, calling into question their environmental friendliness. No-effect on crops is also possible but less observed. Unlike other crops (e.g., wheat, maize and bean), only onion seems resistant to microplastics. Crop uptake of micro/nanoplastic demands a clear benchmark to ensure food-safety. Furthermore, mixed effects are observed on soil functions. Alternation in soil enzymes and litter decomposition can affect nutrients and organic matter biogeochemistry. Hydrophobicity can be induced by increasing evaporation. Shifts in microbial community structure and activities are inevitable.

Exploring Vitamin B1 Cycling and Its Connections to the Microbial Community in the North Atlantic Ocean

Vitamin B1 (thiamin) is an essential coenzyme for all cells. Recent findings from experimental cell biology and genome surveys have shown that thiamin cycling by plankton is far more complex than was previously understood. Many plankton cells cannot produce thiamin (are auxotrophic) and obligately require an exogenous source of thiamin or one or more of 5 different thiamin-related compounds (TRCs). Despite this emerging evidence for the evolution among plankton of complex interactions related to thiamin, the influence of TRCs on plankton community structure and productivity are not understood. We report measurements of three dissolved TRCs 4-amino-5-aminomethyl-2-methylpyrimidine (AmMP), 5-(2-hydroxyethyl)-4-methyl-1,3-thiazole-2-carboxylic acid (cHET), and 4-methyl-5-thiazoleethanol (HET) that have never before been assayed in seawater. Here we characterize them alongside other TRCs that were measured previously [thiamin and 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP)], in depth profiles from a latitudinal transect in the north Atlantic in March 2018. TRC concentrations ranged from femptomolar to picomolar. Surface depletion relative to a maximum near the bottom of the euphotic zone and low concentrations at deeper depths were consistent features. Our observations suggest that when bacterial abundance and production are low, TRC concentrations approach a steady state where TRC production and consumption terms are balanced. Standing stocks of TRCs also appear to be positively correlated with bacterial production. However, near the period of peak biomass in the accumulation phase of a bloom we observed an inverse relationship between TRCs and bacterial production, coincident with an increased abundance of Flavobacteria that comparative genomics indicates could be vitamin B1 auxotrophs. While these observations suggest that the dissolved pool of TRCs is often at steady state, with TRC production and consumption balanced, our data suggests that bloom induced shifts in microbial community structure and activity may cause a decoupling between TRC production and consumption, leading to increased abundances of some populations of bacteria that are putatively vitamin B1 auxotrophs.