Distinct Microbial Groups Research Articles

Exploring the Microbial Mosaic: Insights into Composition, Diversity, and Environmental Drivers in the Pearl River Estuary Sediments.

River estuaries are dynamic and complex ecosystems influenced by various natural processes, including climatic fluctuations and anthropogenic activities. The Pearl River Estuary (PRE), one of the largest in China, receives significant land-based pollutants due to its proximity to densely populated areas and urban development. This study aimed to characterize the composition, diversity, and distribution patterns of sediment microbial communities (bacteria, archaea, and eukaryotes) and investigated the connection with environmental parameters within the PRE and adjacent shelf. Physicochemical conditions, such as oxygen levels, nitrogen compounds, and carbon content, were analyzed. The study found that the microbial community structure was mainly influenced by site location and core depth, which explained approximately 67% of the variation in each kingdom. Sites and core depths varied in sediment properties such as organic matter content and redox conditions, leading to distinct microbial groups associated with specific chemical properties of the sediment, notably C/N ratio and NH4+ concentration. Despite these differences, certain dominant taxonomic groups were consistently present across all sites: Gammaproteobacteria in bacteria; Bathyarchaeia, Nitrososphaeria, and Thermoplasmata in archaea; and SAR in Eukaryota. The community diversity index was the highest in the bacteria kingdom, while the lowest values were observed at site P03 across the three kingdoms and were significantly different from all other sites. Overall, this study highlights the effect of depth, core depth, and chemical properties on sediment microbiota composition. The sensitivity and dynamism of the microbiota, along with the possibility of identifying specific markers for changes in environmental conditions, is valuable for managing and preserving the health of estuaries and coastal ecosystems.

The effect of natural products used as pesticides on the soil microbiota: OECD 216 nitrogen transformation test fails to identify effects that were detected via q-PCR microbial abundance measurement.

Natural products present an environmentally attractive alternative to synthetic pesticides which have been implicated in the off-target effect. Currently, the assessment of pesticide toxicity on soil microorganisms relies on the OECD 216 N transformation assay (OECD stands for the Organisation Economic Co-operation and Development, which is a key international standard-setting organisation). We tested the hypotheses that (i) the OECD 216 assay fails to identify unacceptable effects of pesticides on soil microbiota compared to more advanced molecular and standardized tests, and (ii) the natural products tested (dihydrochalcone, isoflavone, aliphatic phenol, and spinosad) are less toxic to soil microbiota compared to a synthetic pesticide compound (3,5-dichloraniline). We determined the following in three different soils: (i) ammonium (NH4 +) and nitrate (NO3 -) soil concentrations, as dictated by the OECD 216 test, and (ii) the abundance of phylogenetically (bacteria and fungi) and functionally distinct microbial groups [ammonia-oxidizing archaea (AOA) and bacteria (AOB)] using quantitative polymerase chain reaction (q-PCR). All pesticides tested exhibited limited persistence, with spinosad demonstrating the highest persistence. None of the pesticides tested showed clear dose-dependent effects on NH4 + and NO3 - levels and the observed effects were <25% of the control, suggesting no unacceptable impacts on soil microorganisms. In contrast, q-PCR measurements revealed (i) distinct negative effects on the abundance of total bacteria and fungi, which were though limited to one of the studied soils, and (ii) a significant reduction in the abundance of both AOA and AOB across soils. This reduction was attributed to both natural products and 3,5-dichloraniline. Our findings strongly advocate for a revision of the current regulatory framework regarding the toxicity of pesticides to soil microbiota, which should integrate advanced and well-standardized tools. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Effects of environmental parameters on spatial and temporal distribution of marine microbial communities in the southern Black Sea

The Black Sea is a unique environment with strong and permanent vertical stratification, with a thin layer of oxic zone above and a permanent anoxic zone below. Few high-throughput genomic surveys have been conducted to examine microbiota in the Black Sea. Yet, there is no study on the seasonal and vertical variation in microbial community compositions, driving forces and mechanisms of community assembly. In this study, seasonal, vertical, and spatial microbial assemblages were studied in terms of diversity, abundance, and community structure using 16S rRNA metabarcoding. 16S rRNA metabarcoding confirmed seasonal changes in microbial communities and the presence of distinct microbial groups among different water layers. Taxa belonging to Cyanobiaceae contributed a large fraction of the total biomass and were the most abundant autotrophic bacteria found across the whole water column, including hydrogen sulfide-containing anoxic zone. Temperature, salinity, water density, conductivity, light, chlorophyll-a, O2, NO3, NH3, PO4, Si, and H2S had a significant influence on the vertical bacterial community assemblages. The copper mine discharge system at 180 m did not affect microbial community structure and composition. Temperature seemed to be a primary factor in the variance between shallow depths. In conclusion, the lack of light, low dissolved oxygen levels, and low temperature do not restrict microbial diversity, as proven by the higher diversity observed in deeper zones. Wastewater in Black Sea region may be discharged into the Black Sea to depth of 180 m or deeper without impacting microbial ecology.

Long-read assembled metagenomic approaches improve our understanding on metabolic potentials of microbial community in mangrove sediments

BackgroundMangrove wetlands are coastal ecosystems with important ecological features and provide habitats for diverse microorganisms with key roles in nutrient and biogeochemical cycling. However, the overall metabolic potentials and ecological roles of microbial community in mangrove sediment are remained unanswered. In current study, the microbial and metabolic profiles of prokaryotic and fungal communities in mangrove sediments were investigated using metagenomic analysis based on PacBio single-molecule real time (SMRT) and Illumina sequencing techniques.ResultsComparing to Illumina short reads, the incorporation of PacBio long reads significantly contributed to more contiguous assemblies, yielded more than doubled high-quality metagenome-assembled genomes (MAGs), and improved the novelty of the MAGs. Further metabolic reconstruction for recovered MAGs showed that prokaryotes potentially played an essential role in carbon cycling in mangrove sediment, displaying versatile metabolic potential for degrading organic carbons, fermentation, autotrophy, and carbon fixation. Mangrove fungi also functioned as a player in carbon cycling, potentially involved in the degradation of various carbohydrate and peptide substrates. Notably, a new candidate bacterial phylum named as Candidatus Cosmopoliota with a ubiquitous distribution is proposed. Genomic analysis revealed that this new phylum is capable of utilizing various types of organic substrates, anaerobic fermentation, and carbon fixation with the Wood-Ljungdahl (WL) pathway and the reverse tricarboxylic acid (rTCA) cycle.ConclusionsThe study not only highlights the advantages of HiSeq-PacBio Hybrid assembly for a more complete profiling of environmental microbiomes but also expands our understanding of the microbial diversity and potential roles of distinct microbial groups in biogeochemical cycling in mangrove sediment.-S53N_3zEPEL_LmTMdKdCcVideo

Size matters: biochemical mineralization and microbial incorporation of dicarboxylic acids in soil

The transformation and turnover time of medium- to long-chain dicarboxylic acids (DCA) in soil is regulated by microbial uptake and mineralization. However, the chain length of n-alkyl lipids may have a remarkable influence on its microbial utilization and mineralization and therefore on the formation of stable soil organic carbon from e.g. leave- needle- and root-derived organic matter during decomposition. To investigate their size dependent mineralization and microbial incorporation, four DCA of different chain lengths (12–30 carbon atoms), that were 13C labeled at each of their terminal carboxylic groups, were applied to the Ah horizon of a Fluvic Gleysol. Incorporation of 13C into CO2 and in distinct microbial groups classified by phospholipid fatty acid (PLFA) analysis was investigated. Mineralization of DCA and incorporation into PLFA decreased with increasing chain length, and the mineralization rate was highest during the first days of incubation. Half-life time of DCA carbon in soil increased from 7.6 days for C12 DCA to 86.6 days for C18 DCA and decreased again to 46.2 days for C22 DCA, whereas C30 DCA had the longest half-life time. Rapid and efficient uptake of C12 DCA as an intact molecule was observable. Gram-negative bacteria incorporated higher amounts of DCA-derived 13C compared to other microbial groups, especially compared to actinomycetes and fungi during the first phase of incubation. However, the incorporation of C12 DCA derived 13C into the PLFA of actinomycetes, and fungi increased steadily during the entire incubation time, suggesting that those groups take up the 13C label from necromass of bacteria that used the C12 DCA for formation of their lipids before.

Ecological risk assessment and identification of the distinct microbial groups in heavy metal-polluted river sediments.

To assess the health of river ecosystems, it is essential to quantify the ecological risk of heavy metals in river sediments and the structure of microbial communities. As important tributaries of the Tuo River in the upper reaches of the Yangtze River, the Mianyuan River and the Shiting River, are closely related to the economic development and human daily life in the region. This study assessed the ecological risks of heavy-metal-polluted river sediments, the heavy-metal-driven bacterial communities were revealed, and the relationships between the ecological risks and the identical bacterial communities were discussed. The Cd content was significantly greater than the environmental background value, leading to a serious pollution and very high ecological risk at the confluence of the two rivers and the upper reaches of the Mianyuan River. Microbial community analysis showed that Rhodobacter, Nocardioides, Sphingomonas, and Pseudarthrobacter were the dominant bacterial genera in the sediments of the Shiting River. However, the dominant bacterial genera in the Mianyuan River were Kouleothrix, Dechloromonas, Gaiella, Pedomicrobium, and Hyphomicrobium. Mantel test results showed (r = 0.5977, P = 0.005) that the Cd, As, Zn, Pb, Cr, and Cu were important factors that influenced differences in the distribution of sediment bacterial communities Mianyuan and Shiting rivers. A correlation heatmap showed that heavy metals were negatively correlated for most bacterial communities, but some bacterial communities were tolerant and showed a positive correlation. Overall, the microbial structure of the river sediments showed a diverse spatial distribution due to the influence of heavy metals. The results will improve the understanding of rivers contaminated by heavy metals and provide theoretical support for conservation and in situ ecological restoration of river ecosystems.

Metagenomic Screening for Lipolytic Genes Reveals an Ecology-Clustered Distribution Pattern.

Lipolytic enzymes are one of the most important enzyme types for application in various industrial processes. Despite the continuously increasing demand, only a small portion of the so far encountered lipolytic enzymes exhibit adequate stability and activities for biotechnological applications. To explore novel and/or extremophilic lipolytic enzymes, microbial consortia in two composts at thermophilic stage were analyzed using function-driven and sequence-based metagenomic approaches. Analysis of community composition by amplicon-based 16S rRNA genes and transcripts, and direct metagenome sequencing revealed that the communities of the compost samples were dominated by members of the phyla Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes, and Chloroflexi. Function-driven screening of the metagenomic libraries constructed from the two samples yielded 115 unique lipolytic enzymes. The family assignment of these enzymes was conducted by analyzing the phylogenetic relationship and generation of a protein sequence similarity network according to an integrated classification system. The sequence-based screening was performed by using a newly developed database, containing a set of profile Hidden Markov models, highly sensitive and specific for detection of lipolytic enzymes. By comparing the lipolytic enzymes identified through both approaches, we demonstrated that the activity-directed complements sequence-based detection, and vice versa. The sequence-based comparative analysis of lipolytic genes regarding diversity, function and taxonomic origin derived from 175 metagenomes indicated significant differences between habitats. Analysis of the prevalent and distinct microbial groups providing the lipolytic genes revealed characteristic patterns and groups driven by ecological factors. The here presented data suggests that the diversity and distribution of lipolytic genes in metagenomes of various habitats are largely constrained by ecological factors.

Wheat Production Alters Soil Microbial Profiles and Enhances Beneficial Microbes in Double-Cropping Soybean

Plant-parasitic nematodes represent a substantial constraint on global food security by reducing the yield potential of all major crops. The soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) is widely distributed across important soybean production areas of the U.S., being the major soybean yield-limiting factor, especially in the Midwestern U.S. Double cropped (DC) soybean is commonly planted following winter wheat. We previously reported double-cropping soybean fields with reduced SCN counts compared to fallow at both R1 growth stage (beginning of flowering) (−31.8%) and after soybean harvest (−32.7%). To test if higher counts of beneficial and SCN antagonistic microorganisms could be correlated with the suppression of SCN in fields previously planted with wheat, three field locations with noted SCN suppression were selected for a metagenomics study. Ten subplots were selected (5 wheat and 5 fallow pre-soybean) from each location. A total of 90 soil samples were selected: 3 fields ×2 treatments × 3 timepoints × 5 replications. Three DNA markers targeted distinct microbial groups: bacteria (16S V4-V5), fungi (ITS2), and Fusarium (tef1). Amplicons were sequenced using an Illumina MiSeq platform (300 bp paired-end). Sequencing datasets were processed in R using the DADA2 pipeline. Fungal populations were affected by location in all sampling periods and differed significantly between DC and fallow plots at soybean planting and after harvest (P &amp;lt; 0.001). Several enriched fungal and bacterial taxa in wheat plots, including Mortierella, Exophiala, Conocybe, Rhizobacter spp., and others, were previously reported to parasitize SCN and other plant-parasitic nematodes, suggesting a potential role of beneficial microbes in suppression of SCN in soybean fields double-cropped with wheat.

Impact of Cashew (Anacardium occidentale L.) by-Product on Composition and Metabolic Activity of Human Colonic Microbiota In Vitro Indicates Prebiotic Properties.

Cashew apple by-product (CAB) is an important agro-industrial waste still underutilized, although it has been characterized as source of a variety of nutrients and bioactive compounds. This study evaluated the capability of freeze-dried CAB (FCAB) submitted to a simulated gastrointestinal digestion of inducing changes in relative abundance of distinct microbial groups found as part of human colonic microbiota, as well as in pH and short-chain fatty acid production during a 24-h in vitro fermentation using a pooled human fecal inocula. FCAB increased the relative abundance of Bifidobacterium and Lactobacillus/Enterococcus during colonic fermentation, besides to decrease the relative abundance of Bacteroides/Prevotella, Eubacterium rectale/Clostridium coccoides, and Clostridium histolyticum. FCAB increased the counts of lactic acid bacteria and decreased the counts of Enterobacteriaceae during colonic fermentation. Furthermore, FCAB decreased pH and increased the production of short-chain fatty acids in colonic fermentation media. These effects could be linked to contents of dietary fibers and the presence of fructans and different phenolic compounds found in FCAB. These results showed that FCAB induced positive alterations in composition and metabolic activity of human colonic microbiota in vitro, which indicate prebiotic properties.

Effect of digestate application on microbial respiration and bacterial communities' diversity during bioremediation of weathered petroleum hydrocarbons contaminated soils

Digestate is an organic by-product of biogas production via anaerobic digestion processes and has a great potential as soil fertilizer due to concentrated nutrients. In this study, we examined digestate as a potential nutrient and microbial seeding for bioremediation of weathered (aged) petroleum hydrocarbon contaminated soils. We analysed 6 different treatments in microcosm using two industrial soils having different textures: a clay rich soil and a sandy soil. After 30 days of incubation, the highest total petroleum hydrocarbons (TPH) removal was observed in microcosms containing digestate together with bulking agent (17.8% and 12.7% higher than control in clay rich soil and sandy soil, respectively) or digestate together with immobilized bacteria (13.4% and 9% higher than control in clay rich soil and sandy soil, respectively). After digestate application microbial respiration was enhanced in sandy soil and inhibited in clay rich soil due to aggregates formation. After bulking agent addition to clay rich soil aggregates size was reduced and oxygen uptake was improved. Application of digestate to soil resulted in the development of distinct microbial groups in amended and non-amended soils. Genera containing species able to degrade TPH like Acinetobacter and Mycobacterium were abundant in digestate and in soil amended with digestate. Quantification of alkB genes, encoding alkane monoxygenase, revealed high concentration of these genes in digestate bacterial community. After application of digestate, the level of alkB genes significantly increased in soils and remained high until the end of the treatment. The study revealed great potential of digestate as a nutrient and bacteria source for soil bioremediation.

Food for microorganisms: Position-specific 13C labeling and 13C-PLFA analysis reveals preferences for sorbed or necromass C

Sorption to mineral surfaces is one of the most important processes contributing to soil organic matter (SOM) stabilization. While this stabilization is commonly attributed to inaccessibility of the sorbed SOM to microorganisms, recent findings have revealed increased metabolic efficiency from sorbed substrates. The application of position-specifically 13C labeled sorbed tracer, combined with compound-specific 13C analysis of phospholipid fatty acids (PLFA), enables determination of whether this higher efficiency is due to a metabolic shift in a) the whole microbial community or b) microbial specialists adapted to sorbed C sources.To assess metabolic changes induced by sorption in individual microbial groups, we added uniformly and position-specifically 13C labeled alanine to a loamy Luvisol and incubated the soil samples for 10 days. Two different amendments were compared: i) alanine sorbed to sterilized soil, and ii) free alanine in solution. Incorporation of C from individual alanine positions was evaluated in distinct microbial groups classified by 13C-PLFA analysis.Most of the microbial groups took up sorbed and free alanine equally. The metabolic pattern was also similar in most microbial groups: incorporation of C from carboxylic C-1 into PLFA was negligible, whereas C from the amino-bound C-2 and the methyl C-3 were preferentially incorporated into PLFA. This pattern reflects the basic microbial metabolism of C3 molecules - fast mineralization of C-1 via pyruvate decarboxylation. Only fungi incorporated more C from sorbed than free alanine into their PLFA. Their metabolic pattern also revealed a more complex metabolization via gluconeogenesis, followed by pentose-phosphate pathway.While the incorporation into most microbial groups’ PLFA remained stable or decreased over 10 days, the 13C in Actinobacteria PLFA increased up to 7 times from day 1 to day 10. This strong 13C increase in Actinobacteria was explained by their uptake of secondary substrates derived from microbial necromass or secretion products.This experiment showed that the more efficient metabolization of sorbed substrates is the work of microbial specialists: While uniform labeling revealed the higher incorporation of sorbed than free substrate into fungus PLFAs, position-specific labeling allowed the reconstruction of metabolic changes triggered by sorption of the substrate.To assess changes in the transformation pathways of individual microbial groups caused by sorption, we added uniformly and position-specifically 13C and 14C labeled alanine—a common amino acid in soil—in two ways: i) sorbed to sterilized soil (loamy Luvisol) or ii) free in solution, and incubated for 10 days. Microbial incorporation of alanine’s individual C positions was evaluated in distinct microbial groups classified by 13C-PLFA analysis.Most of the microbial groups were able to take up sorbed and free alanine equally. The metabolic pattern also remained similar in most microbial groups: the C from carboxylic C-1 was nearly not incorporated into PLFA, whereas the C from the amino-bound (C-2) and the methylic C-3 were preferentially incorporated into PLFA of microorganisms. This reflects the basic microbial metabolism of C3 molecules via glycolysis. Only fungi incorporated more C from sorbed than free alanine into their PLFA. Their metabolic pattern also revealed a much more complex metabolization via gluconeogenesis, followed by pentose-phosphate pathway.While the incorporation into all microbial groups’ PLFA remained stable or decreased over 10 days, the 13C in Actinomycetes PLFA increased up to 7 times from day 1 to day 10. This strong 13C increase in Actinomycetes was explained by their uptake of secondary substrates derived from microbial necromass or secretion products.While uniform labeling was able to reveal the preference of fungi for sorbed versus free substrates, position-specific labeling allowed the reconstruction of metabolic changes triggered by sorption of the substrate and reflected a metabolic preference in fungi for sorbed, charged monomers.

Spatial Interaction of Archaeal Ammonia-Oxidizers and Nitrite-Oxidizing Bacteria in an Unfertilized Grassland Soil.

Interrelated successive transformation steps of nitrification are performed by distinct microbial groups – the ammonia-oxidizers, comprising ammonia-oxidizing archaea (AOA) and bacteria (AOB), and nitrite-oxidizers such as Nitrobacter and Nitrospira, which are the dominant genera in the investigated soils. Hence, not only their presence and activity in the investigated habitat is required for nitrification, but also their temporal and spatial interactions. To demonstrate the interdependence of both groups and to address factors promoting putative niche differentiation within each group, temporal and spatial changes in nitrifying organisms were monitored in an unfertilized grassland site over an entire vegetation period at the plot scale of 10 m2. Nitrifying organisms were assessed by measuring the abundance of marker genes (amoA for AOA and AOB, nxrA for Nitrobacter, 16S rRNA gene for Nitrospira) selected for the respective sub-processes. A positive correlation between numerically dominant AOA and Nitrospira, and their co-occurrence at the same spatial scale in August and October, suggests that the nitrification process is predominantly performed by these groups and is restricted to a limited timeframe. Amongst nitrite-oxidizers, niche differentiation was evident in observed seasonally varying patterns of co-occurrence and spatial separation. While their distributions were most likely driven by substrate concentrations, oxygen availability may also have played a role under substrate-limited conditions. Phylogenetic analysis revealed temporal shifts in Nitrospira community composition with an increasing relative abundance of OTU03 assigned to sublineage V from August onward, indicating its important role in nitrite oxidation.

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations.

Multiple models describe the formation and evolution of distinct microbial phylogenetic groups. These evolutionary models make different predictions regarding how adaptive alleles spread through populations and how genetic diversity is maintained. Processes predicted by competing evolutionary models, for example, genome-wide selective sweeps vs gene-specific sweeps, could be captured in natural populations using time-series metagenomics if the approach were applied over a sufficiently long time frame. Direct observations of either process would help resolve how distinct microbial groups evolve. Here, from a 9-year metagenomic study of a freshwater lake (2005–2013), we explore changes in single-nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in 30 bacterial populations. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied by >1000-fold among populations. SNP allele frequencies also changed dramatically over time within some populations. Interestingly, nearly all SNP variants were slowly purged over several years from one population of green sulfur bacteria, while at the same time multiple genes either swept through or were lost from this population. These patterns were consistent with a genome-wide selective sweep in progress, a process predicted by the ‘ecotype model' of speciation but not previously observed in nature. In contrast, other populations contained large, SNP-free genomic regions that appear to have swept independently through the populations prior to the study without purging diversity elsewhere in the genome. Evidence for both genome-wide and gene-specific sweeps suggests that different models of bacterial speciation may apply to different populations coexisting in the same environment.

Microbial mobilization of rare earth elements (REE) from mineral solids—A mini review

In the light of an expected supply shortage of rare earth elements (REE) measures have to be undertaken for an efficient use in all kinds of technical, medical, and agricultural applications as well as—in particular—in REE recycling from post-use goods and waste materials. Biologically- based methods might offer an alternative and supplement to physico-chemical techniques for REE recovery and recycling. A wide variety of physiologically distinct microbial groups have the potential to be applied for REE bioleaching form solid matrices. This source is largely untapped until today. Depending of the type of organism, the technical process (including a series of influencing factors), the solid to be treated, and the target element, leaching efficiencies of 80 to 90% can be achieved. Bioleaching of REEs can help in reducing the supply risk and market dependency. Additionally, the application of bioleaching techniques for the treatment of solid wastes might contribute to the conversion towards a more sustainable and environmental friendly economy.

Biochemical pathways of amino acids in soil: Assessment by position-specific labeling and 13C-PLFA analysis

Microbial utilization is a key transformation process of soil organic matter (SOM). For the first time, position-specific 13C labeling was combined with compound-specific 13C-PLFA analysis to trace metabolites of two amino acids in microbial groups and to reconstruct detailed biochemical pathways. Short-term transformation was assessed by applying position-specifically 13C labeled alanine and glutamic acid to soil in a field experiment. Microbial utilization of the amino acids' functional groups was quantified by 13C incorporation in total microbial biomass and in distinct microbial groups classified by 13C-PLFA.Loss from PLFAs was fastest for the highly oxidized carboxyl group of both amino acids, whereas the reduced C positions, e.g. C3–5, were preferentially incorporated into microorganisms and their PLFAs. The incorporation of C from alanines' C2 position into the cell membrane of gram negative bacteria was higher by more than one order of magnitude than into all other microbial groups. Whereas C2 of alanine was still bound to C3 at day 3, the C2 and C3 positions were partially split at day 10. In contrast, the C2 of glutamic acid was lost faster from PLFAs of all microbial groups. The divergence index, which reflects relative incorporation of one position to the incorporation of C from all positions in a molecule, revealed that discrimination between positions is highest in the initial reactions and decreases with time.Reconstruction of microbial transformation pathways showed that the C2 position of alanine is lost faster than its C3 position regardless of whether the molecule is used ana- or catabolically. Glutamic acid C2 is incorporated into PLFAs only by two out of eight microbial groups (fungi and part of gram positive prokaryotes). Its incorporation in PLFA can only be explained by either the utilization of the glyoxolate bypass or the transformation of glutamic acid into aspartate prior to being fed into the citric acid cycle. During these pathways, no C is lost as CO2 but neither is energy produced, making them typical C deficiency pathways. Glutamic acid is therefore a promising metabolic tracer in regard to ecophysiology of cells and therefore changing environmental conditions.Analyzing the fate of individual C atoms by position-specific labeling allows insight into the mechanisms and kinetics of microbial utilization by various microbial groups. This approach will strongly improve our understanding of soil C fluxes.

Legacies of native climate regime govern responses of boreal soil microbes to litter stoichiometry and temperature

Temperature and substrate stoichiometry can influence soil organic matter (SOM) decomposition, but whether their interactive effect is significant remains unclear. This study explores linkages between substrate stoichiometry and warming-induced patterns of microbial carbon (C) mineralization in boreal forest soils via replacements of native litterfall with Oi material possessing distinct δ13C and C:N. Following 120 day incubations of soils from sites similar except for mean annual temperature, we examined exo-enzyme activities, microbial biomass, and δ13C of respired CO2 and individual phospholipid fatty acids (PLFA) to identify microbial community and decay responses to these experimental manipulations. In accordance with stoichiometric theory, we hypothesized that warming-induced increases in microbial use of naturally low C:N Oea materials and fungal incorporation of Oea would be enhanced when available Oi material exhibited relatively high C:N. These hypotheses were only partially supported. At the warmer site, higher C:N Oi was linked to an enhanced, warming-induced decline in Oi-derived CO2, lower C:N Oi prompted an increase in the warming-induced increase in phenol oxidase activities, and the interaction between temperature and Oi C:N had no influence on the relative abundances or activities of distinct microbial groups. In contrast, responses to Oi C:N and temperature at the cooler site were evident only via changes in the structure and substrate preference of the active microbial community; we observed a ∼25% increase in the incorporation of low C:N Oi into fungi relative to bacteria in these soils when they were incubated at a relatively high temperature. The data emphasize the importance of native climate imposing a legacy effect on how these microbial communities respond to temperature and substrate stoichiometry, by governing those communities' adaptive characteristics and the climate-related composition of the SOM on which they depend. That legacy effect is reflected in patterns of decay and in the relative abundances of microbial groups that both decay and generate SOM.

Warming alters routing of labile and slower-turnover carbon through distinct microbial groups in boreal forest organic soils

Our understanding of the mechanisms driving the response of soil organic carbon (SOC) pools to warming, though critical for predicting climate feedbacks, remains limited. Here we report results from a warming experiment using O-horizon soils from two mesic, boreal forest sites with contrasting climate regimes. We replaced extant Oi soil horizons, or litterfall C, with another coniferous Oi possessing a distinct δ13C signature, and tracked the net incorporation of the replaced Oi and, by difference, Oea-C into soil microbial phospholipid fatty acids (PLFA) following 120-day incubations at 15 °C and 20 °C. We demonstrate how regional climate (site effects) and experimental warming (temperature effects) influence microbial incorporation of Oi versus slower-turnover Oea SOC pools. Microbial biomass, estimated from total PLFA, increased by 32–60% with temperature and was 20–42% higher within soils from the warmer versus cooler site, congruent with increased mineralization in those soils. The proportion of Gram-positive bacterial PLFA-C derived from Oi-C more than doubled and coincided with a reduction in the incorporation of Oi-C into fungal relative to bacterial PLFA with warming and in soils from the warmer site. Mirroring the relative decrease in fungal incorporation of Oi-C, warming led to an increase of 22–31% in the proportion of fungal PLFA-C derived from the Oea-C, consistent with the increased incorporation of this slower-turnover SOC pool in soils from the warmer site. The increase in microbial biomass and shift in routing of Oi and Oea pools through PLFA indicate that warming preferentially increases fungal mineralization of more slow-turnover C pools in these boreal organic soils. Shifts in microbial substrate routing and biomass increases with warming observed here underscore the potential importance of changing proportions of microbial biomass remnant contributions to SOC pools with climate warming.

Removal of ammonium via simultaneous nitrification–denitrification nitrite-shortcut in a single packed-bed batch reactor

A polyurethane packed-bed-biofilm sequential batch reactor was fed with synthetic substrate simulating the composition of UASB reactor effluents. Two distinct ammonia nitrogen concentrations (125 and 250 mg l −1) were supplied during two sequential long-term experiments of 160 days each (320 total). Cycles of 24 h under intermittent aeration for periods of 1 h were applied, and ethanol was added as a carbon source at the beginning of each anoxic period. Nitrite was the main oxidized nitrogen compound which accumulated only during the aerated phases of the batch cycle. A consistent decrease of nitrite concentration started always immediately after the interruption of oxygen supply and addition of the electron donor. Removal to below detection limits of all nitrogen soluble forms was always observed at the end of the 24 h cycles for both initial concentrations. Polyurethane packed-bed matrices and ethanol amendments conferred high process stability. Microbial investigation by cloning suggested that nitrification was carried out by Nitrosomonas-like species whereas denitrification was mediated by unclassified species commonly observed in denitrifying environments. The packed-bed batch bioreactor favored the simultaneous colonization of distinct microbial groups within the immobilized microbial biomass. The biofilm was capable of actively oxidizing ammonium and denitrification at high ratios in intermittent intervals within 24 h cycles.

Apple Root stocks and Pre-plant Soil Treatments Alter Soil Microbial Community Composition in a New York Orchard

Apple (Malu ×domestica) replant disease (ARD) is a soil-borne disease syndrome of complex etiology that occurs worldwide when establishing new orchards in old fruit-growing sites. Methyl bromide (MB) has been an effective soil fumigant to control ARD, but safer alternatives to MB are needed. We evaluated soil microbial communities, tree growth, and fruit yield for three pre-plant soil treatments (compost amendment, soil treatment with a broad-spectrum fumigant, and untreated controls), and five clonal rootstocks (M7, M26, CG6210, CG30, and G16), in an apple replant site at Ithaca, N.Y. Molecular fingerprinting (PCR-DGGE) techniques were used to study soil microbial community composition of root-zone soil of the different soil treatments and rootstocks. Tree caliper, shoot growth, and yield were measured annually from 2002–04. Among the five rootstocks we compared, trees on CG6210 had the most growth and yield, while trees on M26 had the least growth and yield. Soil treatments altered soil microbial communities during the year after pre-plant treatments, and each treatment was associated with distinct microbial groups in hierarchical cluster analyses. However, those differences among fungal and bacterial communities diminished during the second year after planting, and soil fungal communities equilibrated faster than bacterial communities. Pre-plant soil treatments altered bulk-soil microbial community composition, but those shifts in soil microbial communities had no obvious correlation with tree performance. Rootstock genotypes were the dominant factor in tree performance after 3 years of observations, and different rootstocks were associated with characteristic bacterial, pseudomonad, fungal, and oomycetes communities in root-zone soil.

Stable-isotope probing as a tool in microbial ecology.

Microorganisms are responsible for driving the biogeochemical cycling of elements on Earth. Despite their importance and vast diversity, the taxonomic identity of the microorganisms involved in any specific process has usually been confined to that small fraction of the microbiota that has been isolated and cultivated. The recent coupling of molecular biological methods with stable-isotope abundance in biomarkers has provided a cultivation-independent means of linking the identity of bacteria with their function in the environment. Here we show that 13C-DNA, produced during the growth of metabolically distinct microbial groups on a 13C-enriched carbon source, can be resolved from 12C-DNA by density-gradient centrifugation. DNA isolated from the target group of microorganisms can be characterized taxonomically and functionally by gene probing and sequence analysis. Application of this technique to investigate methanol-utilizing microorganisms in soil demonstrated the involvement of members of two phylogenetically distinct groups of eubacteria; the alpha-proteobacterial and Acidobacterium lineages. Stable-isotope probing thus offers a powerful new technique for identifying microorganisms that are actively involved in specific metabolic processes under conditions which approach those occurring in situ.