Abundance Of Microbial Groups Research Articles

Analysis of the Probiotic Potential of Lactiplantibacillus plantarum LB1_P46 Isolated from the Mexican Fermented Pulque Beverage: A Functional and Genomic Analysis.

The traditional Mexican fermented beverage pulque has been considered a healthy product for treating gastrointestinal disorders. Lactic acid bacteria (LAB) have been identified as one of the most abundant microbial groups during pulque fermentation. As traditional pulque is consumed directly from the fermentation vessel, the naturally associated LABs are ingested, reaching the consumer's small intestine alive, suggesting their potential probiotic capability. In this contribution, we assayed the probiotic potential of the strain of Lactiplantibacillus plantarum LB1_P46 isolated from pulque produced in Huitzilac, Morelos State, Mexico. The characterization included resistance to acid pH (3.5) and exposure to bile salts at 37 °C; the assay of the hemolytic activity and antibiotic resistance profiling; the functional traits of cholesterol reduction and β-galactosidase activity; and several cell surface properties, indicating that this LAB possesses probiotic properties comparable to other LAB. Additionally, this L. plantarum showed significance in in vitro antimicrobial activity against several Gram-negative and Gram-positive bacteria and in vivo preventive anti-infective capability against Salmonella in a BALB/c mouse model. Several functional traits and probiotic activities assayed were correlated with the corresponding enzymes encoded in the complete genome of the strain. The genome mining for bacteriocins led to the identification of several bacteriocins and a ribosomally synthesized and post-translationally modified peptide encoding for the plantaricin EF. Results indicated that L. plantarum LB1_P46 is a promising probiotic LAB for preparing functional non-dairy and dairy beverages.

Phenotypic and genomic characterization of Bathyarchaeum tardum gen. nov., sp. nov., a cultivated representative of the archaeal class Bathyarchaeia.

Bathyarchaeia are widespread in various anoxic ecosystems and are considered one of the most abundant microbial groups on the earth. There are only a few reports of laboratory cultivation of Bathyarchaeia, and none of the representatives of this class has been isolated in pure culture. Here, we report a sustainable cultivation of the Bathyarchaeia archaeon (strain M17CTs) enriched from anaerobic sediment of a coastal lake. The cells of strain M17CTs were small non-motile cocci, 0.4-0.7 μm in diameter. The cytoplasmic membrane was surrounded by an S-layer and covered with an outermost electron-dense sheath. Strain M17CTs is strictly anaerobic mesophile. It grows at 10-45°C (optimum 37°C), at pH 6.0-10.0 (optimum 8.0), and at NaCl concentrations of 0-60 g l-1 (optimum 20 g l-1). Growth occurred in the presence of methoxylated aromatic compounds (3,4-dimethoxybenzoate and vanillate) together with complex proteinaceous substrates. Dimethyl sulfoxide and nitrate stimulated growth. The phylogenomic analysis placed strain M17CTs to BIN-L-1 genus-level lineage from the BA1 family-level lineage and B26-1 order-level lineage (former subgroup-8) within the class Bathyarchaeia. The complete genome of strain M17CTs had a size of 2.15 Mb with a DNA G + C content of 38.1%. Based on phylogenomic position and phenotypic and genomic properties, we propose to assign strain M17CTs to a new species of a novel genus Bathyarchaeum tardum gen. nov., sp. nov. within the class Bathyarchaeia. This is the first sustainably cultivated representative of Bathyarchaeia. We propose under SeqCode the complete genome sequence of strain M17CTs (CP122380) as a nomenclatural type of Bathyarchaeum tardum, which should be considered as a type for the genus Bathyarchaeum, which is proposed as a type for the family Bathyarchaeaceae, order Bathyarchaeales, and of the class Bathyarchaeia.

Effects of natural non-volcanic CO2 leakage on soil microbial community composition and diversity

Geological carbon capture and storage (CCS) can reduce anthropogenic CO2 emissions, but questions exist about impacts at the surface if CO2 leaks from deep storage reservoirs. To examine potential impacts on soils, previous studies have investigated the geochemistry and microbiology of volcanic soils hosting high fluxes of CO2 rich gas. This study builds on those previous investigations by considering impacts of CO2 leakage at a non-volcanic site, where deep geogenic CO2 leaks from a cracked well casing. At the site, we collected 26 soil cores adjacent to soil gas monitoring wells. Based on measured CO2 fluxes, the soil samples fall into two groups 1) high CO2 (flux = 304.6 ± 272.1 g m−2 d−1, conc. = 29.1 ± 34 %) and 2) low CO2 (flux = 15.8 ± 6.1 g m−2 d−1, conc. = 0.8 ± 0.9 %). Soil pH was significantly lower (p < 0.05) in high flux group samples (4.6 ± 0.3) than the low flux ones (5.3 ± 0.7). Beta diversity calculations using 16S rRNA gene sequences and redundancy analysis (RDA) revealed clear clustering of microbial communities relative to CO2 flux and significant correlations of community composition with pH and organic carbon content. In the high flux soils, abundant microbial groups included Acidobacteriota, Ktedonobacteria, and SC-I-84 in the phylum Proteobacteria, as well as Nitrososphaeria, a genus of ammonia oxidizing archaea. Compared to volcanic sites described previously, our non-volcanic site had slight differences in soil geochemical properties and gradual shifts in community compositions between CO2 hotspots and background locations. Moreover, the elevated abundance of SC-I-84 has not been reported in studies of volcanic sites. This study improves our ability to predict potential environmental impacts of geological CCS by expanding the range of conditions over which existing CO2 leakage has been observed.

DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms.

Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of 13C, 18O, or 15N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labelled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labelled populations by targeted gene analysis. Such approaches usually involved fingerprint-based analyses or sequencing clone libraries containing 16S rRNA genes or functional marker gene amplicons. Although molecular fingerprinting remains a valuable approach for rapid confirmation of isotope labelling, recent advances in sequencing technology mean that it is possible to obtain affordable and comprehensive amplicon profiles, or even metagenomes and metatranscriptomes from SIP experiments. Not only can the abundance of microbial groups be inferred from metagenomes, but researchers can bin, assemble, and explore individual genomes to build hypotheses about the metabolic capabilities of labelled microorganisms. Analysis of labelled mRNA is a more recent advance that can provide independent metatranscriptome-based analysis of active microorganisms. The power of metatranscriptomics is that mRNA abundance often correlates closely with the corresponding activity of encoded enzymes, thus providing insight into microbial metabolism at the time of sampling. Together, these advances have improved the sensitivity of SIP methods and allowed using labelled substrates at environmentally relevant concentrations. Particularly as methods improve and costs continue to drop, we expect that the integration of SIP with multiple omics-based methods will become prevalent components of microbial ecology studies, leading to further breakthroughs in our understanding of novel microbial populations and elucidation of the metabolic function of complex microbial communities. In this chapter, we provide protocols for obtaining labelled DNA, RNA, and proteins that can be used for downstream omics-based analyses.

High-resolution vertical biogeochemical profiles in the hyporheic zone reveal insights into microbial methane cycling

Abstract. Facing the challenges of climate change, policy making relies on sound greenhouse gas (GHG) budgets. Rivers and streams emit large quantities of the potent GHG methane (CH4), but their global impact on atmospheric CH4 concentrations is highly uncertain. In situ data from the hyporheic zone (HZ), where most CH4 is produced and some of it can be oxidized to CO2, are lacking for an accurate description of CH4 production and consumption in streams. To address this, we recorded high-resolution depth-resolved geochemical profiles at five different locations in the stream bed of the river Moosach, southern Germany. Specifically, we measured pore-water concentrations and stable carbon isotopes (δ13C) of dissolved CH4 as well as relevant electron acceptors for oxidation with a 1 cm vertical depth resolution. Findings were interpreted with the help of a numerical model, and 16S rRNA gene analyses added information on the microbial community at one of the locations. Our data confirm with pore-water CH4 concentrations of up to 1000 µmol L−1 that large quantities of CH4 are produced in the HZ. Stable isotope measurements of CH4 suggest that hydrogenotrophic methanogenesis represents a dominant pathway for CH4 production in the HZ of the river Moosach, while a relatively high abundance of a novel group of methanogenic archaea, the Candidatus “Methanomethyliales” (phylum Candidatus “Verstraetearchaeota”), indicate that CH4 production through H2-dependent methylotrophic methanogenesis might also be an important CH4 source. Combined isotopic and modeling results clearly implied CH4 oxidation processes at one of the sampled locations, but due to the steep chemical gradients and the close proximity of the oxygen and nitrate reduction zones, no single electron acceptor for this process could be identified. Nevertheless, the numerical modeling results showed potential not only for aerobic CH4 oxidation but also for anaerobic oxidation of CH4 coupled to denitrification. In addition, the nitrate–methane transition zone was characterized by an increased relative abundance of microbial groups (Crenothrix, NC10) known to mediate nitrate and nitrite-dependent methane oxidation in the hyporheic zone. This study demonstrates substantial CH4 production in hyporheic sediments, a potential for aerobic and anaerobic CH4 oxidation, and underlines the high spatiotemporal variability in this habitat.

Association analyses of host genetics, root-colonizing microbes, and plant phenotypes under different nitrogen conditions in maize.

The root-associated microbiome (rhizobiome) affects plant health, stress tolerance, and nutrient use efficiency. However, it remains unclear to what extent the composition of the rhizobiome is governed by intraspecific variation in host plant genetics in the field and the degree to which host plant selection can reshape the composition of the rhizobiome. Here, we quantify the rhizosphere microbial communities associated with a replicated diversity panel of 230 maize (Zea mays L.) genotypes grown in agronomically relevant conditions under high N (+N) and low N (-N) treatments. We analyze the maize rhizobiome in terms of 150 abundant and consistently reproducible microbial groups and we show that the abundance of many root-associated microbes is explainable by natural genetic variation in the host plant, with a greater proportion of microbial variance attributable to plant genetic variation in -N conditions. Population genetic approaches identify signatures of purifying selection in the maize genome associated with the abundance of several groups of microbes in the maize rhizobiome. Genome-wide association study was conducted using the abundance of microbial groups as rhizobiome traits, and n=622 plant loci were identified that are linked to the abundance of n=104 microbial groups in the maize rhizosphere. In 62/104 cases, which is more than expected by chance, the abundance of these same microbial groups was correlated with variation in plant vigor indicators derived from high throughput phenotyping of the same field experiment. We provide comprehensive datasets about the three-way interaction of host genetics, microbe abundance, and plant performance under two N treatments to facilitate targeted experiments toward harnessing the full potential of root-associated microbial symbionts in maize production.

Rare microbial populations as sensitive indicators of bacterial community dissimilarity under different agricultural management practices

ABSTRACT Revealing the composition and role of rare and abundant microbial groups is crucial to understand ecosystem processes and function. In 2018, we characterized soil bacterial community, abundant (AMPs) and rare microbial populations (RMPs) with mineral fertilizer and mineral fertilizer combined with straw return under continuous maize (Zea mays L.) and soybean (Glycine max Merr.)-maize rotation systems in a Mollisol in Northeast China. The results showed that the effects of fertilization on total bacterial community, AMPs and RMPs were greater than cropping systems. The cropping systems had a stronger effect on α diversity of bacterial community than fertilization. The RMPs accounted for 50.1% of the relative abundance and contributed 64.3% to the community dissimilarity. The RMPs accounted for 96.7% of the amount of operational taxonomic units (OTUs), thus became the most important contributors to community diversity. The OTUs with lower relative abundance had a narrower niche range, indicating that rare OTUs were more easily affected by habitat uniqueness. The RMPs were important contributors to chemoheterotrophs and were more closely correlated with variations in soil functions than AMPs. Our results provided deep insight into the ecological role of RMPs, which is useful for rational management and improving agricultural ecosystem sustainability.

Changes in soil carbon and nitrogen stocks and microbial community after forest conversion in a subtropical region

ABSTRACT The quantitative understanding of different land use is still limited. We selected typical natural secondary forest (NSF) and Chinese-fir plantation (CPF) in southern China to quantify changes of soil carbon (C) and nitrogen (N) as well as microbial community composition after forest conversion in the soil profile up to 60 cm. The results showed that soil CN stocks and all functional microbial groups in CPF were significantly lower in the topsoil but did not change in the subsoil (10–60 cm) compared to those in NSF after 24 years conversion. Soil C/N ratio did not differ between the two forests for all soil depths. Correlation analysis showed that the abundance of microbial groups in the topsoil was significantly related to soil organic carbon, total nitrogen and forest floor N stock. Redundancy analysis showed that available N, especially NO3 −–N, was the most dominant factor influencing the microbial community composition. These findings suggest that the plantation could inhibit the accumulation of soil C and N, but the changes are primarily evident in surface soil after conversion. The study improves our understanding of soil C, N and microbial community changes under different land uses and provides insights into sustainable management of Chinese forests.

Improved detection of disease-associated gut microbes using 16S sequence-based biomarkers

BackgroundSequencing partial 16S rRNA genes is a cost effective method for quantifying the microbial composition of an environment, such as the human gut. However, downstream analysis relies on binning reads into microbial groups by either considering each unique sequence as a different microbe, querying a database to get taxonomic labels from sequences, or clustering similar sequences together. However, these approaches do not fully capture evolutionary relationships between microbes, limiting the ability to identify differentially abundant groups of microbes between a diseased and control cohort. We present sequence-based biomarkers (SBBs), an aggregation method that groups and aggregates microbes using single variants and combinations of variants within their 16S sequences. We compare SBBs against other existing aggregation methods (OTU clustering and Microphenoor DiTaxa features) in several benchmarking tasks: biomarker discovery via permutation test, biomarker discovery via linear discriminant analysis, and phenotype prediction power. We demonstrate the SBBs perform on-par or better than the state-of-the-art methods in biomarker discovery and phenotype prediction.ResultsOn two independent datasets, SBBs identify differentially abundant groups of microbes with similar or higher statistical significance than existing methods in both a permutation-test-based analysis and using linear discriminant analysis effect size. . By grouping microbes by SBB, we can identify several differentially abundant microbial groups (FDR <.1) between children with autism and neurotypical controls in a set of 115 discordant siblings. Porphyromonadaceae, Ruminococcaceae, and an unnamed species of Blastocystis were significantly enriched in autism, while Veillonellaceae was significantly depleted. Likewise, aggregating microbes by SBB on a dataset of obese and lean twins, we find several significantly differentially abundant microbial groups (FDR<.1). We observed Megasphaera andSutterellaceae highly enriched in obesity, and Phocaeicola significantly depleted. SBBs also perform on bar with or better than existing aggregation methods as features in a phenotype prediction model, predicting the autism phenotype with an ROC-AUC score of .64 and the obesity phenotype with an ROC-AUC score of .84.ConclusionsSBBs provide a powerful method for aggregating microbes to perform differential abundance analysis as well as phenotype prediction. Our source code can be freely downloaded from http://github.com/briannachrisman/16s_biomarkers.

A new non-steady-state mass balance model for quantifying microbiome responses to disturbances in wastewater bioreactors

Herein we proposed an ecology model, based on a non-steady-state mass balance (16S rRNA MiSeq reads normalized by volatile suspended solids), to quantify microbiome responses to disturbances in wastewater bioreactors. Rather than focusing on the most abundant microbial groups commonly used in the literature, the goal of the model was to identify active species within the community. The model incorporated the temporal changes of operational taxonomic units following a disturbance, through considering the density and type of genotypes in the influent entering the bioreactor, in the effluent leaving the bioreactor, growing in the bioreactor, and in the waste sludge discharged from the bioreactor continuously or instantaneously, as well as the prior microbial community and the sludge characteristics. One application of this model demonstrated that significant differences existed between the key populations responding to an increasing organic loading rate and the dominant species in a high-rate thermophilic upflow anaerobic sludge blanket reactor.

Microbial response to the presence of invasive ctenophore Mnemiopsis leidyi in the coastal waters of the Northeastern Adriatic

Seasonal blooms of the invasive ctenophore Mnemiopsis leidyi have been recorded throughout the Adriatic Sea, affecting the ecosystem and its pelagic resources. Gelatinous organisms such as M. leidyi release significant quantities of excreta as labile and surface active dissolved organic carbon (DOC) that supports the microbial activity.The effects of M. leidyi's presence on heterotrophic prokaryotes (HP), cyanobacteria (CB) and heterotrophic nanoflagellates (HNF) were investigated at five locations in the coastal waters of Rovinj-Rovigno (northern Adriatic) during intensive blooms in September 2019. Additionally, circulation in the study area was examined using available current measurements and a hydrodynamic model. In September, low-pass filtered currents near the surface were mostly directed toward S-SE reaching 25 cm/s, indicating the presence of the Istrian Coastal Countercurrent (ICCC).Ctenophores displayed a patchy spatial distribution from 0.05 to 100 M. leidyi individuals per m3. When ctenophore density in the swarms surpassed 1 individual per m3, the change in the abundances of microbial groups became evident. The lowest microbial densities and lowest concentrations of dissolved and particulate organic carbon (DOC and POC) and surface-active substances occurred in the absence of M. leidyi, while the highest were within the swarms.We hypothesise that HP utilises the available DOC enhancing the remineralisation of organic matter. Finally, greater availability of HNF's prey (HP and CB) leads to an increase in their abundance.This study illustrates how the release of surface-active DOC during intensive M. leidyi's blooms can stimulate the microbial loop. The current system with the ICCC prevailing in September enables the spreading of M. leidyi from its hypothetic origin in an open sea gyre towards the coast. Bora wind episodes may initiate and favour this type of circulation. In these conditions, M. leidyi agglomerates in large numbers along the coast, enabling the accumulation of organic matter and altering the abundance of pico- and nanoplankton.

Unveiling Taxonomic Diversity and Functional Composition Differences of Microbial Mat Communities Through Comparative Metagenomics

Microbial mats are stratified systems of microorganisms that have served as models to study diverse ecological functions. Comparing the unique and shared characteristics between different microbial mats could shed new light on the biodiversity, functionality and genetic potential of these habitats. In this study, the taxonomic diversity of a microbial mat from the Araro hot springs (Trans-Mexican volcanic belt) was explored and compared with the metagenomes of microbial mats from Cuatro Ciénegas (Mexico), Guerrero Negro (Mexico), Shark Bay (Australia), Yellowstone (USA), and Diamond Fork (USA). The thermal Araro microbial mat was dominated by the phyla Chloroflexi (particularly Chloroflexus), Cyanobacteria, and Proteobacteria. Chlorobium was abundant at Diamond Fork; whereas Thermus, Synechococcus, and Bacillus were found at the remaining locations together with less abundant microbial groups. Alpha diversity indices were highest in Araro, Cuatro Ciénegas, and Shark Bay. Principal component analysis and hierarchical clustering separated Araro from the remaining microbial mats. SEED subsystems revealed carbohydrate metabolism, amino acids, and derivatives to be dominant functions in most mats, while protein and DNA metabolism were prevalent in Araro. Sequences related to biogeochemical cycles of N, Fe, C, O, and S were observed in all mats except Yellowstone (O cycle only), suggesting the presence of different trophic groups. In summary, the six metagenomes exhibit important taxonomic and functional differences, which could be related to their environmental and physicochemical adaptations.

A review on microbial diversity and genetic markers involved in methanogenic degradation of hydrocarbons: futuristic prospects of biofuel recovery from contaminated regions.

Microbial activities within oil reservoirs have adversely impacted the world's majority of oil by lowering its quality, thereby increasing its recovery and refining cost. Moreover, conventional method of extraction leaves behind nearly two-thirds of the fossil fuels in the oil fields. This huge potential can be extracted if engineered methanogenic consortium is adapted to convert the hydrocarbons into natural gas. This process involves conversion of crude oil hydrocarbons into methanogenic substrates by syntrophic and fermentative bacteria, which are subsequently utilized by methanogens to produce methane. Microbial diversity of such environments supports the viability of this process. This review illuminates the potentials of abundant microbial groups such as Syntrophaceae, Anaerolineaceae, Clostridiales and Euryarchaeota in petroleum hydrocarbon-related environment, their genetic markers, biochemical process and omics-based bioengineering methods involved in methane generation. Increase in the copy numbers of catabolic genes during methanogenesis highlights the prospect of developing engineered biofuel recovery technology. Several lab-based methanogenic consortia from depleted petroleum reservoirs and microcosm studies so far would not be enough for field application without the advent of multi-omics-based technologies to trawl out the bottleneck parameters of the enhanced fuel recovery process. The adaptability of efficient consortium of versatile hydrocarbonoclastic and methanogenic microorganisms under environmental stress conditions is further needed to be investigated. The improved process might hold the potential of methane extraction from petroleum waste like oil tank and refinery sludge, oil field deposits, etc. What sounds as biodegradation could be a beginning of converting waste into wealth by recovery of stranded energy assets.

CPR and DPANN Have an Overlooked Role in Corals' Microbial Community Structure.

Understanding how microbial communities are structured in coral holobionts is important to estimate local and global impacts and provide efficient environment management strategies. Several studies investigated the relationship between corals and their microbial communities, including the environmental drivers of shifts in this relationship, associated with diseases and coral cover loss. However, these studies are often geographically or taxonomically restricted and usually focused on the most abundant microbial groups, neglecting the rare biosphere, including archaea in the group DPANN and the recently discovered bacterial members of the candidate phyla radiation (CPR). Although it is known that rare microbes can play essential roles in several environments, we still lack understanding about which taxa comprise the rare biosphere of corals' microbiome. Here, we investigated the host-related and technical factors influencing coral microbial community structure and the importance of CPR and DPANN in this context by analyzing more than a hundred coral metagenomes from independent studies worldwide. We show that coral genera are the main biotic factor shaping coral microbial communities. We also detected several CPR and DPANN phyla comprising corals' rare biosphere for the first time and showed that they significantly contribute to shaping coral microbial communities.

Litter decomposition was retarded by understory removal but was unaffected by thinning in a Chinese fir [Cunninghamia lanceolata (Lamb.) Hook] plantation

Thinning and understory removal, which are commonly used in forest management, are expected to affect litter decomposition. However, little is known about how litter decomposition rates change in stands subject to both thinning and understory removal. This knowledge gap is urgent to be filled because the two practices are often applied simultaneously. In the present study, an experiment containing a complete factorial combination of thinning and understory removal was arranged in a Chinese fir (Cunninghamia lanceolata) plantation. Litter decomposition rate was determined by using litter bags, and litter bags with different mesh sizes (0.1 mm and 2 mm) were used to identify the effect of soil mesofauna on decomposition. The temperature, moisture, and microbial abundance of surface soil were also measured. Results showed that thinning did not change litter decomposition rate, partly because of the unresponsive soil temperature, moisture, and abundance of microbial groups following thinning. Understory removal markedly restricted litter mass loss by more than 20%. Despite an obvious decrease in soil microbial abundance following understory removal, this should not account for why understory removal lowered litter decomposition rate, because this negative effect on litter mass loss disappeared when soil mesofauna was excluded. In addition, no interaction between thinning and understory removal was detected on litter decomposition. We emphasized that (1) Understory removal retard litter decomposition by suppressing the activity of soil mesofauna rather than by reducing microbial abundance; (2) Understory removal caused an equal reduction in litter mass loss regardless of thinning treatment. We believe that these results provide an important guidance for evaluating the effect of thinning and understory removal on some ecological processes associated with litter decomposition (i.e. soil formation and CO2 emission from the soil to the atmosphere) in a fir plantation.

Impact of soil leachate on microbial biomass and diversity affected by plant diversity

High plant diversity is usually linked with high soil microbial diversity, which is hypothesized to be attributed to a high diversity of components in the soil leachate, but experimental evidence is scarce. The aim of this study was to determine if the variation in soil leachate caused by plant diversity could affect the soil microbial community. A microcosm experiment was conducted to determine the effect of plant diversity on the soil microbial community by measuring soil leachate in a gradient of plant richness from levels 1 (one species) to 3 (three species). Plant richness significantly affected the diversity of soil leachate and microbial communities. The amount and diversity of soil leachate, microbial biomass carbon (C), basal respiration, β-1,4-glucosidase activity, β-1,4-N-acetylglucosaminidase activity, bacterial biomass, fungal biomass, total microorganism biomass, and microbial diversity (Shannon diversity index and evenness) were highest at richness level 3. Changes in the microbial community were best explained by variation in the amount and diversity of leachate. Linear regression and correlation analyses indicated that leachate diversity had a close association with microbial Shannon diversity and evenness, whereas leachate amount had a close association with microbial biomass C, total microbial biomass, bacterial biomass, enzyme activities, and abundance of microbial groups. An ordinary least squares multiple regression and the structural equation model demonstrated that leachate amount had a greater effect on microbial biomass than leachate diversity, which had a greater impact on microbial Shannon diversity and evenness. Our results indicate that plant diversity drives changes in soil microbial communities by altering the amount and diversity of leachate in the soil. The diversity of soil leachate determined the diversity of the microbial community to some extent.

Seasonal dynamics alter taxonomical and functional microbial profiles in Pampa biome soils under natural grasslands.

Soil microbial communities’ assembly is strongly tied to changes in temperature and moisture. Although microbial functional redundancy seems to overcome taxonomical composition changes, the sensitivity and resilience of soil microbial communities from subtropical regions in response to seasonal variations are still poorly understood. Thus, the development of new strategies for biodiversity conservation and sustainable management require a complete understanding of the soil abiotic process involved in the selection of microbial taxa and functions. In this work, we used state of the art molecular methodologies (Next Generation Sequencing) to compare the taxonomic (metataxonomics) and functional (metatranscriptomics) profiles among soil samples from two subtropical natural grasslands located in the Pampa biome, Brazil, in response to short-term seasonal variations. Our data suggest that grasslands maintained a stable microbial community membership along the year with oscillation in abundance. Apparently soil microbial taxa are more susceptible to natural climatic disturbances while functions are more stable and change with less intensity along the year. Finally, our data allow us to conclude that the most abundant microbial groups and functions were shared between seasons and locations reflecting the existence of a stable taxonomical and functional core microbiota.

Effects of permafrost thaw-subsidence on soil bacterial communities in the southern Qinghai-Tibetan Plateau

Permafrost thaws cause ground subsidence as the ground ice melts and drains away. Little is known about the effects of this permafrost thaw subsidence on bacterial communities. In this study, using Illumina sequencing methods, we investigated the structure of bacterial communities in the upper 50 cm of the soil in a typical permafrost thaw subsidence area on the southern Qinghai-Tibetan plateau. The micro topographies in the study area were classified as control, collapsing, and subsided types. Results showed that the organic carbon content in the collapsing areas was slightly lower than that in the control areas, while there was a substantial decrease in the subsided areas, with a loss of 23.6 ± 13.2% of organic carbon. The microbial carbon contents showed the highest values in collapsing areas. For all three types of soils, the most abundant microbial groups were Proteobacteria, Acidobacteria, and Bacteroidetes. The Non-metricmultidimensionalscaling (NMDS) results showed that the bacterial communities were different in the subsided areas than in the control and collapsing areas. In the control and collapsing areas, the soil bacterial communities showed a clear vertical distribution pattern with depth, which was not apparent in the subsided areas. The bacterial communities also correlated with soil variables such as carbon, moisture, nitrogen contents, and the C:N ratio. The ground subsidence can greatly change these variables. The results suggested that permafrost thaw subsidence had important effects on microbial communities via the changes of soil properties.

Thaumarchaeal ecotype distributions across the equatorial Pacific Ocean and their potential roles in nitrification and sinking flux attenuation

AbstractThaumarchaea are among the most abundant microbial groups in the ocean, but controls on their abundance and the distribution and metabolic potential of different subpopulations are poorly constrained. Here, two ecotypes of ammonia‐oxidizing thaumarchaea were quantified using ammonia monooxygenase (amoA) genes across the equatorial Pacific Ocean. The shallow, or water column “A” (WCA), ecotype was the most abundant ecotype at the depths of maximum nitrification rates, and its abundance correlated with other biogeochemical indicators of remineralization such as NO3 : Si and total Hg. Metagenomes contained thaumarchaeal genes encoding for the catalytic subunit of the urease enzyme (ureC) at all depths, suggesting that members of both WCA and the deep, water column “B” (WCB) ecotypes may contain ureC. Coupled urea hydrolysis‐ammonia oxidation rates were similar to ammonia oxidation rates alone, suggesting that urea could be an important source of ammonia for mesopelagic ammonia oxidizers. Potential inducement of metal limitation of both ammonia oxidation and urea hydrolysis was demonstrated via additions of a strong metal chelator. The water column inventory of WCA was correlated with the depth‐integrated abundance of WCB, with both likely controlled by the flux of sinking particulate organic matter, providing strong evidence of vertical connectivity between the ecotypes. Further, depth‐integrated amoA gene abundance and nitrification rates were correlated with particulate organic nitrogen flux measured by contemporaneously deployed sediment traps. Together, the results refine our understanding of the controls on thaumarchaeal distributions in the ocean, and provide new insights on the relationship between material flux and microbial communities in the mesopelagic.

Contrasting effects of biochar on N2O emission and N uptake at different N fertilizer levels on a temperate sandy loam

Biochar has been frequently suggested as an amendment to improve soil quality and mitigate climate change. To investigate the optimal management of nitrogen (N) fertilization, we examined the combined effect of biochar and N fertilizer on plant N uptake and N2O emissions in a cereal rotation system in a randomized two-factorial field experiment on a sandy loam soil in Brandenburg, Germany. The biochar treatment received 10Mgha−1 wood-derived biochar in September 2012. Four levels of N fertilizer, corresponding to 0, 50%, 100%, 130% of the recommended fertilizer level, were applied in winter wheat (Triticum aestivum L.)) and winter rye (Secale cereal L.) in 2013 and 2014 followed by the catch crop oil radish (Raphanus sativus L. var. oleiformis). Biomass and N uptake of winter wheat and winter rye were significantly affected by the level of N fertilizer but not by biochar. For N uptake of oil radish an interaction effect was observed for biochar and N fertilizer. Without applied fertilizer, 39% higher N uptake was found in the presence of biochar, accompanied by higher soil NH4+ content and elevated cumulative CO2 emissions. At 130% of the recommended fertilizer level, 16% lower N uptake and lower cumulative N2O emissions were found in the biochar-mediated treatment. No significant change in abundance of microbial groups and nosZ gene were observed. Our results highlight that biochar can have a greenhouse gas mitigation effect at high levels of N supply and may stimulate nutrient uptake when no N is supplied.