Respiration of 13C-labeled substrates added to soil in the field and subsequent 16S rRNA gene analysis of 13C-labeled soil DNA

Composition and metabolism of microbial communities in soil pores

Delineation of microbial habitats within the soil matrix and characterization of their environments and metabolic processes are crucial to understand soil functioning, yet their experimental identification remains persistently limited. We combined single- and triple-energy X-ray computed microtomography with pore specific allocation of 13C labeled glucose and subsequent stable isotope probing to demonstrate how long-term disparities in vegetation history modify spatial distribution patterns of soil pore and particulate organic matter drivers of microbial habitats, and to probe bacterial communities populating such habitats. Here we show striking differences between large (30-150 µm Ø) and small (4-10 µm Ø) soil pores in (i) microbial diversity, composition, and life-strategies, (ii) responses to added substrate, (iii) metabolic pathways, and (iv) the processing and fate of labile C. We propose a microbial habitat classification concept based on biogeochemical mechanisms and localization of soil processes and also suggests interventions to mitigate the environmental consequences of agricultural management.

Effects of municipal waste compost on microbial biodiversity and energy production in terrestrial microbial fuel cells

Microbial Fuel Cells (MFCs) transform organic matter into electricity through microbial electrochemical reactions catalysed on anodic and cathodic half-cells. Terrestrial MFCs (TMFCs) are a bioelectrochemical system for bioelectricity production as well as soil remediation. In TMFCs, the soil is the ion-exchange electrolyte, whereas a biofilm on the anode oxidises organic matter through electroactive bacteria. Little is known of the overall microbial community composition in a TMFC, which impedes complete exploitation of the potential to generate energy in different soil types. In this context, an experiment was performed to reveal the prokaryotic community structure in single chamber TMFCs with soil in the presence and absence of a municipal waste compost (3% w/v). The microbial community was assessed on the anode and cathode and in bulk soil at the end of the experiment (54 days). Moreover, TMFC electrical performance (voltage and power) was also evaluated over the experimental period, varying the external resistance to improve performance. Compost stimulated soil microbial activity, in line with a general increase in voltage and power. Significant differences were observed in the microbial communities between initial soil conditions and TMFCs, and between the anode, cathode and bulk soil in the presence of the compost. Several electroactive genera (Bacillus, Fulvivirga, Burkholdeira and Geobacter) were found at the anode in the presence of compost. Overall, the use of municipal waste compost significantly increased the performance of the MFCs in terms of electrical power and voltage generated, not least thanks to the selective pressure towards electroactive bacteria on the anode.

Advances and perspectives of using stable isotope probing (SIP)-based technologies in contaminant biodegradation

Stable isotope probing (SIP) is a powerful tool to study microbial community structure and function in both nature and engineered environments. Coupling with advanced genomics and other techniques, SIP studies have generated substantial information to allow researchers to draw a clearer picture of what is occurring in complex microbial ecosystems. This review provides an overview of the advances of SIP-based technologies over time, summarizes the status of SIP applications to contaminant biodegradation, provides critical perspectives on ecological interactions within the community, and important factors (controllable and non-controllable) to be considered in SIP experimental designs and data interpretation. Current trend and perspectives of adapting SIP techniques for environmental applications are also discussed.

Investigating bacterial coupled assimilation of fertilizer‑nitrogen and crop residue‑carbon in upland soils by DNA-qSIP

Microbial immobilization of fertilizer nitrogen (N) can effectively reduce N losses in soil. However, the effects of crop residue on microbial assimilation of fertilizer-N and the underlying microbial mechanisms in upland soils are unclear. We evaluated the influence of maize residue (¹³C) addition on the microbial assimilation of ammonium-N (¹⁵N) in DNA from fertilizer, and quantified the bacterial ¹³C or ¹⁵N assimilation by quantitative stable isotope probing (DNA-qSIP). We found that the straw addition did increase total microbial assimilation of ammonium from fertilizer during the 2-week incubation. However, bacterial taxa varied in their responses to straw addition: Bacteriodetes and Proteobacteria accounted for large fractions of ammonium assimilation and their N assimilations were increased, while N assimilations of Acidobacteria were decreased. We revealed that highly ¹³C-labeled taxa were the main contributors of N assimilation under straw addition. The straw primarily enhanced the contributions of bacterial taxa to ammonium assimilation through increasing the extent of N assimilation, or enhancing the abundance of the N-assimilating bacterial taxa. Overall, our study elucidated an interaction between microbial assimilation of fertilizer-N and straw-C, showing a close element coupling of the keystone functional microbial taxa in N immobilization driven by organic carbon.

Responses of soil respiration and microbial community structure to fertilizer and irrigation regimes over 2 years in temperate vineyards in North China

Fertilizer and irrigation regimes can profoundly affect soil carbon (C) emissions, which influence soil organic carbon (SOC) storage. However, information regarding the effects of fertilizer and irrigation management on the components of soil respiration (Rs) and the underlying microbial community characteristics in vineyard ecosystems remains limited. Therefore, a 2-year field experiment was conducted in a wine-grape vineyard (WGV) and a table-grape vineyard (TGV). Each vineyard included two fertilizer and irrigation regimes: farmers' practice (FP) and recommended practice (RP). The trenching method was employed to separate Rs into heterotrophic respiration (Rh) and autotrophic respiration (Ra). Additionally, the SOC storage and soil microbial community structure at 0-20 cm soil depth were determined after the 2-year experiment. The results showed that the fertilizer and irrigation regimes caused no effect on Ra. Compared with the FP treatment in WGV and TGV, the RP treatment significantly (P < 0.05) decreased the average daily Rh by 15.13 % and 17.11 %, which contributed to the annual Rs values at the whole-vineyard scale decreased by 8.93 % and 11.78 %, respectively. Besides, compared with the initial value, the SOC storage under RP treatment were effectively increased by 6.39 % and 6.33 % in WGV and TGV, respectively. Low annual total Rh was partially ascribed to the significant (P < 0.05) decline in Proteobacteria and Bacteroidetes relative abundance, thus reducing the decomposition rate of SOC. Compared with WGV, the fertilizer and water input was higher in the TGV, which resulted in the annual total Rs and Rh values at the whole-vineyard scale was increased by 11.53 % and 15.74 %, respectively, while the annual total Ra was decreased by 18.83 % due to the lower grapevine density and more frequent summer pruning. Overall, RP treatment was found to be a suitable strategy for reducing soil C emissions and benefiting SOC storage in vineyards around North China.

Temporal Variations Rather than Long-Term Warming Control Extracellular Enzyme Activities and Microbial Community Structures in the High Arctic Soil

In Arctic soils, warming accelerates decomposition of organic matter and increases emission of greenhouse gases (GHGs), contributing to a positive feedback to climate change. Although microorganisms play a key role in the processes between decomposition of organic matter and GHGs emission, the effects of warming on temporal responses of microbial activity are still elusive. In this study, treatments of warming and precipitation were conducted from 2012 to 2018 in Cambridge Bay, Canada. Soils of organic and mineral layers were collected monthly from June to September in 2018 and analyzed for extracellular enzyme activities and bacterial community structures. The activity of hydrolases was the highest in June and decreased thereafter over summer in both organic and mineral layers. Bacterial community structures changed gradually over summer, and the responses were distinct depending on soil layers and environmental factors; water content and soil temperature affected the shift of bacterial community structures in both layers, whereas bacterial abundance, dissolved organic carbon, and inorganic nitrogen did so in the organic layer only. The activity of hydrolases and bacterial community structures did not differ significantly among treatments but among months. Our results demonstrate that temporal variations may control extracellular enzyme activities and microbial community structure rather than the small effect of warming over a long period in high Arctic soil. Although the effects of the treatments on microbial activity were minor, our study provides insight that microbial activity may increase due to an increase in carbon availability, if the growing season is prolonged in the Arctic.

Variation in Soil Bacterial and Fungal Community Composition at Different Successional Stages of a Broad-Leaved Korean Pine Forest in the Lesser Hinggan Mountains

Soil microorganisms are an integral part of the soil and are highly sensitive to environmental changes. The shift in plant community and soil properties following forest succession may cause differences in soil bacterial and fungal community composition. Some studies suggested following the succession of the community, the species composition tends to switch from r-strategy groups to k-strategy groups. However, generalization on the changing pattern has not been worked out. Three forests at an early-, intermediate-, and late-stage (ES, IS, LS) of the succession of broad-leaved Korean pine forest in the Lesser Hinggan Mountains were surveyed to study the variation in soil bacterial and fungal community composition as the succession proceeds. Soil microbial community composition and related soil factors were analyzed by systematic sampling. Significant differences in soil microbial community composition were detected between forests at different stages. The bacterial diversity increased, while the fungal diversity decreased (p < 0.05) from the early to the late successional forest. The fungi to bacteria ratio (F/B) and the (Proteobacteria + Bacteroidetes) to (Actinobacteria + Acidobacteria) ratio increased substantially with succession (p < 0.05). At the phylum level, Bacteroidetes, Ascomycota and Mortierellomycota were dominant in the ES forest, while Actinobacteria and Basidiomycota were prevalent in the LS forest. At the class level, Gammaproteobacteria, Acidobacteriia, Bacteroidia, Sordariomycetes and Mortierellomycetes were dominant in the ES forest, whereas Subgroup_6, Agaricomycetes, Geminibasidiomycetes and Tremellomycetes were dominant in the LS forest. Soil water content (SWC) and available phosphorus (AP) had significant effects on the bacterial community composition (p < 0.05). Soil organic carbon (SOC), total nitrogen (TN), the carbon–nitrogen ratio (C/N), total potassium (TK) and SWC had significant effects on the fungal community composition (p < 0.05). SOC and TN were positively correlated with r-strategy groups (p < 0.05) and were significantly negatively correlated with k-strategy groups (p < 0.05). Our results suggest that the soil bacterial and fungal community composition changed significantly in forests across the successional stages, and the species composition switched from r-strategy to k-strategy groups. The bacterial and fungal community diversity variation differed in forests across the successional stages. The changes in soil organic carbon and nitrogen content resulted in the shifting of microbial species with different ecological strategies.

Marine Vertebrates Impact the Bacterial Community Composition and Food Webs of Antarctic Microbial Mats

The biological activity of marine vertebrates represents an input of nutrients for Antarctic terrestrial biota, with relevant consequences for the entire ecosystem. Even though microbial mats assemble most of the biological diversity of the non-marine Antarctica, the effects of the local macrofauna on these microecosystems remain understudied. Using 16S rRNA gene sequencing, 13C and 15N stable isotopes, and by characterizing the P and N-derived nutrient levels, we evaluated the effects of penguins and other marine vertebrates on four microbial mats located along the Antarctic Peninsula. Our results show that P concentrations, C/N and N/P ratios, and δ15N values of "penguin-impacted" microbial mats were significantly higher than values obtained for "macrofauna-free" sample. Nutrients derived from penguin colonies and other marine vertebrates altered the trophic interactions of communities within microbial mats, as well as the relative abundance and trophic position of meiofaunal groups. Twenty-nine bacterial families from eight different phyla significantly changed with the presence of penguins, with inorganic nitrogen (NH4 + and NO3 -) and δ15N appearing as key factors in driving bacterial community composition. An apparent change in richness, diversity, and dominance of prokaryotes was also related to penguin-derived nutrients, affecting N utilization strategies of microbial mats and relating oligotrophic systems to communities with a higher metabolic versatility. The interdisciplinary approach of this study makes these results advance our understanding of interactions and composition of communities inhabiting microbial mats from Antarctica, revealing how they are deeply associated with marine animals.

Influence of polyethylene terephthalate microplastic and biochar co-existence on paddy soil bacterial community structure and greenhouse gas emission

Microplastic (MP) contamination is ubiquitous in agricultural soils. As a cost-effective soil amendment, biochar (BC) often coincides with MP exposure. However, little research has been conducted regarding the independent and combined effects of MPs and BC on the soil microbiome and N₂O/CH₄ emissions. Therefore, in this study, polyethylene terephthalate (PET) and wheat straw-derived BC were used, respectively, as representative MP and BC during an entire rice growth period. The high-throughput sequencing results showed that PET alone lowered bacterial diversity by 26.7%, while PET and BC co-existence did not induce apparent change. The relative abundances of some microbes (e.g., Cyanobacteria, Verrucomicrobia, and Bacteroidetes) that are associated with C and N cycling were changed at the phylum and class levels by all the treatments. In comparison with the control, the treatment of BC, PET, and their co-existence reduced the cumulative CH₄ emissions by 50%, 53%, and 61%, respectively. The higher mitigation by BC + PET may be the result of higher soil Eh and a consequently lower methanogenesis functional gene mcrA abundance in the treated soils. In addition, BC and PET alone, as well as their combined treatment, increased the abundance of nitrification genes, enhancing the soil nitrification process. However, the relative contribution of the nitrification process to N₂O emission was possibly lower than that of denitrification, in which the N₂O reductase gene nosZ was found to be the primary gene regulating N₂O emissions. BC alone increased nosZ abundance by 42.3%, thereby showing the potential in suppressing N₂O emission. In contrast, when BC was co-added with PET, the nosZ abundance lowered possibly because of increased soil aeration, and thus its cumulative N₂O emission was 38% higher than the BC treatment. Overall, these results demonstrated that BC and PET function differently in soil ecosystems when they coexisted.

Soil Texture, Sampling Depth and Root Hairs Shape the Structure of ACC Deaminase Bacterial Community Composition in Maize Rhizosphere

Preservation of the phytostimulatory functions of plant growth-promoting bacteria relies on the adaptation of their community to the rhizosphere environment. Here, an amplicon sequencing approach was implemented to specifically target microorganisms with 1-aminocyclopropane-1-carboxylate deaminase activity, carrying the acdS gene. We stated the hypothesis that the relative phylogenetic distribution of acdS carrying microorganisms is affected by the presence or absence of root hairs, soil type, and depth. To this end, a standardized soil column experiment was conducted with maize wild type and root hair defective rth3 mutant in the substrates loam and sand, and harvest was implemented from three depths. Most acdS sequences (99%) were affiliated to Actinobacteria and Proteobacteria, and the strongest influence on the relative abundances of sequences were exerted by the substrate. Variovorax, Acidovorax, and Ralstonia sequences dominated in loam, whereas Streptomyces and Agromyces were more abundant in sand. Soil depth caused strong variations in acdS sequence distribution, with differential levels in the relative abundances of acdS sequences affiliated to Tetrasphaera, Amycolatopsis, and Streptomyces in loam, but Burkholderia, Paraburkholderia, and Variovorax in sand. Maize genotype influenced the distribution of acdS sequences mainly in loam and only in the uppermost depth. Variovorax acdS sequences were more abundant in WT, but Streptomyces, Microbacterium, and Modestobacter in rth3 rhizosphere. Substrate and soil depth were strong and plant genotype a further significant single and interacting drivers of acdS carrying microbial community composition in the rhizosphere of maize. This suggests that maize rhizosphere acdS carrying bacterial community establishes according to the environmental constraints, and that root hairs possess a minor but significant impact on acdS carrying bacterial populations.

Application of wood ash leads to strong vertical gradients in soil pH changing prokaryotic community structure in forest top soil

Wood ash is alkaline and contains base-cations. Application of wood ash to forests therefore counteracts soil acidification and recycle nutrients removed during harvest. Wood ash application to soil leads to strong vertical gradients in physicochemical parameters. Consequently, we designed an experimental system where small-scale vertical changes in soil properties and prokaryotic community structure could be followed after wood ash application. A mixed fly and bottom ash was applied in dosages of 3 and 9 t ha^-1 to the surface of soil mesocosms, simulating a typical coniferous podzol. Soil pH, exchangeable cations and 16S prokaryotic community was subsequently assessed at small depth intervals to 5 cm depth at regular intervals for one year. Wood ash significantly changed the prokaryotic community in the top of the soil column. Also, the largest increases in pH and concentrations of exchangeable cations was found here. The relative abundance of prokaryotic groups directionally changed, suggesting that wood ash favors copiotrophic prokaryotes at the expense of oligotrophic and acidophilic taxa. The effect of wood ash were negligible both in terms of pH- and biological changes in lower soil layers. Consequently, by micro-vertical profiling we showed that wood ash causes a steep gradient of abiotic factors driving biotic changes but only in the top-most soil layers.

Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer

BACKGROUND

Cultivation-independent methods, including metagenomics, are tools for the exploration and discovery of biotechnological compounds produced by microbes in natural environments. Glycoside hydrolases (GHs) enzymes are extremely desired and important in the industry of production for goods and biofuel and removal of problematic biofilms and exopolysaccharide (EPS). Biofilms and EPS are complex, requiring a wide range of enzymes for a complete degradation. The aim of this study was to identify potential GH microbial producers and GH genes with biotechnological potential, using EPS-complex structure (WH15EPS) of Acidobacteria Granulicella sp. strain WH15 as an enrichment factor, in cultivation-independent and cultivation-dependent methods. We performed stable isotope probing (SIP) combined with metagenomics on topsoil litter amended with WH15EPS and coupled solid culture-EPS amended medium with metagenomics.

RESULTS

SIP metagenome analysis of the soil litter demonstrated that phyla Proteobacteria, Actinobacteria, Acidobacteria, and Planctomycetes were the most abundant in WH15EPS amended and unamended treatments. The enrichment cultures in solid culture medium coupled to metagenomics demonstrated an enrichment in Proteobacteria, and the metagenome assembly of this enrichment cultures resulted in 4 metagenome-assembled genomes (MAGs) of microbes with low identity (42-86%) to known microorganisms. Among all carbohydrate-active enzymes (CAZymes) retrieved genes, glycoside transferase (GT) was the most abundant family, either in culture-independent or culture-based metagenome datasets. Within the glycoside hydrolases (GHs), GH13 was the most abundant family in both metagenome datasets. In the "heavy" fraction of the culture-independent metagenome SIP dataset, GH109 (α-N-acetylgalactosaminidases), GH117 (agarases), GH50 (agarases), GH32 (invertases and inulinases), GH17 (endoglucanases), and GH71 (mutanases) families were more abundant in comparison with the controls. Those GH families are affiliated to microorganism that are probably capable to degrade WH15EPS and potentially applicable for biofilm deconstruction. Subsequent in culture-based metagenome, the assembled 4 MAGs (unclassified Proteobacteria) also contained GH families of interest, involving mannosidases, lysozymes, galactosidases, and chitinases.

CONCLUSIONS

We demonstrated that functional diversity induced by the presence of WH15EPS in both culture-independent and culture-dependent approaches was enriched in GHs, such as amylases and endoglucanases that could be applied in chemical, pharmaceutical, and food industrial sectors. Furthermore, WH15EPS may be used for the investigation and isolation of yet unknown taxa, such as unclassified Proteobacteria and Planctomycetes, increasing the number of current cultured bacterial representatives with potential biotechnological traits. Video Abstract.

DNA Stable-Isotope Probing Delineates Carbon Flows from Rice Residues into Soil Microbial Communities Depending on Fertilization

Identifying and understanding the active microbial communities and interactions involved in plant residue utilization are key questions to elucidate the transformation of soil organic matter (SOM) in agricultural ecosystems. Microbial community composition responds strongly to management, but little is known about specific microbial groups involved in plant residue utilization and, consequently, microbial functions under different methods of fertilization. We combined DNA stable-isotope (¹³C) probing and high-throughput sequencing to identify active fungal and bacterial groups degrading residues in soils after 3 years of mineral fertilization with and without manure. Manuring changed the active microbial composition and complexified microbial interactions involved in residue C flow. Most fungal genera, especially Chaetomium, Staphylotrichum, Penicillium, and Aspergillus, responded to residue addition faster in soils that historically had received manure. We generated a valuable library of microorganisms involved in plant residue utilization for future targeted research to exploit specific functions of microbial groups in organic matter utilization and C sequestration.

Decomposition of crop residues in soil is mediated by microorganisms whose activities vary with fertilization. The complexity of active microorganisms and their interactions utilizing residues is impossible to disentangle without isotope applications. Thus, ¹³C-labeled rice residues were employed, and DNA stable-isotope probing (DNA-SIP) combined with high-throughput sequencing was applied to identify microbes active in assimilating residue carbon (C). Manure addition strongly modified microbial community compositions involved in the C flow from rice residues. Relative abundances of the bacterial genus Lysobacter and fungal genus Syncephalis were increased, but abundances of the bacterial genus Streptomyces and fungal genus Trichoderma were decreased in soils receiving mineral fertilizers plus manure (NPKM) compared to levels in soils receiving only mineral fertilizers (NPK). Microbes involved in the flow of residue C formed a more complex network in NPKM than in NPK soils because of the necessity to decompose more diverse organic compounds. The fungal species (Jugulospora rotula and Emericellopsis terricola in NPK and NPKM soils, respectively) were identified as keystone species in the network and may significantly contribute to residue C decomposition. Most of the fungal genera in NPKM soils, especially Chaetomium, Staphylotrichum, Penicillium, and Aspergillus, responded faster to residue addition than those in NPK soils. This is connected with the changes in the composition of the rice residue during degradation and with fungal adaptation (abundance and activity) to continuous manure input. Our findings provide fundamental information about the roles of key microbial groups in residue decomposition and offer important cues on manipulating the soil microbiome for residue utilization and C sequestration in soil.

IMPORTANCE Identifying and understanding the active microbial communities and interactions involved in plant residue utilization are key questions to elucidate the transformation of soil organic matter (SOM) in agricultural ecosystems. Microbial community composition responds strongly to management, but little is known about specific microbial groups involved in plant residue utilization and, consequently, microbial functions under different methods of fertilization. We combined DNA stable-isotope (¹³C) probing and high-throughput sequencing to identify active fungal and bacterial groups degrading residues in soils after 3 years of mineral fertilization with and without manure. Manuring changed the active microbial composition and complexified microbial interactions involved in residue C flow. Most fungal genera, especially Chaetomium, Staphylotrichum, Penicillium, and Aspergillus, responded to residue addition faster in soils that historically had received manure. We generated a valuable library of microorganisms involved in plant residue utilization for future targeted research to exploit specific functions of microbial groups in organic matter utilization and C sequestration.

Stable isotope probing and metagenomics highlight the effect of plants on uncultured phenanthrene-degrading bacterial consortium in polluted soil

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil pollutants. The discovery that plants can stimulate microbial degradation of PAHs has promoted research on rhizoremediation strategies. We combined DNA-SIP with metagenomics to assess the influence of plants on the identity and metabolic functions of active PAH-degrading bacteria in contaminated soil, using phenanthrene (PHE) as a model hydrocarbon. 13C-PHE dissipation was 2.5-fold lower in ryegrass-planted conditions than in bare soil. Metabarcoding of 16S rDNA revealed significantly enriched OTUs in 13C-SIP incubations compared to 12C-controls, namely 130 OTUs from bare soil and 73 OTUs from planted soil. Active PHE-degraders were taxonomically diverse (Proteobacteria, Actinobacteria and Firmicutes), with Sphingomonas and Sphingobium dominating in bare and planted soil, respectively. Plant root exudates favored the development of PHE-degraders having specific functional traits at the genome level. Indeed, metagenomes of 13C-enriched DNA fractions contained more genes involved in aromatic compound metabolism in bare soil, whereas carbohydrate catabolism genes were more abundant in planted soil. Functional gene annotation allowed reconstruction of complete pathways with several routes for PHE catabolism. Sphingomonadales were the major taxa performing the first steps of PHE degradation in both conditions, suggesting their critical role to initiate in situ PAH remediation. Active PHE-degraders act in a consortium, whereby complete PHE mineralization is achieved through the combined activity of taxonomically diverse co-occurring bacteria performing successive metabolic steps. Our study reveals hitherto underestimated functional interactions for full microbial detoxification in contaminated soils.

Soil Properties and Multi-Pollution Affect Taxonomic and Functional Bacterial Diversity in a Range of French Soils Displaying an Anthropisation Gradient

The intensive industrial activities of the twentieth century have left behind highly contaminated wasteland soils. It is well known that soil parameters and the presence of pollutants shape microbial communities. But in such industrial waste sites, the soil multi-contamination with organic (polycyclic aromatic hydrocarbons, PAH) and metallic (Zn, Pb, Cd) pollutants and long-term exposure may induce a selection pressure on microbial communities that may modify soil functioning. The aim of our study was to evaluate the impact of long-term multi-contamination and soil characteristics on bacterial taxonomic and functional diversity as related to the carbon cycle. We worked on 10 soils from northeast of France distributed into three groups (low anthropised controls, slag heaps, and settling ponds) based on their physico-chemical properties (texture, C, N) and pollution level. We assessed bacterial taxonomic diversity by 16S rDNA Illumina sequencing, and functional diversity using Biolog® and MicroResp™ microtiter plate tools. Although taxonomic diversity at the phylum level was not different among the soil groups, many operational taxonomic units were influenced by metal or PAH pollution, and by soil texture and total nitrogen content. Functional diversity was not influenced by PAH contamination while metal pollution selected microbial communities with reduced metabolic functional diversity but more tolerant to zinc. Limited microbial utilisation of carbon substrates in metal-polluted soils was mainly due to the nitrogen content. Based on these two observations, we hypothesised that reduced microbial activity and lower carbon cycle-related functional diversity may have contributed to the accumulation of organic matter in the soils that exhibited the highest levels of metal pollution.

Bacterial and protozoan dynamics upon thawing and freezing of an active layer permafrost soil

The active layer of soil overlaying permafrost in the Arctic is subjected to annual changes in temperature and soil chemistry, which we hypothesize to affect the overall soil microbial community. We investigated changes in soil microorganisms at different temperatures during warming and freezing of the active layer soil from Svalbard, Norway. Soil community data were obtained by direct shotgun sequencing of total extracted RNA. No changes in soil microbial communities were detected when warming from -10 to -2 °C or when freezing from -2 to -10 °C. In contrast, within a few days we observed changes when warming from -2 to +2 °C with a decrease in fungal rRNA and an increase in several OTUs belonging to Gemmatimonadetes, Bacteroidetes and Betaproteobacteria. Even more substantial changes occurred when incubating at 2 °C for 16 days, with declines in total fungal potential activity and decreases in oligotrophic members from Actinobacteria and Acidobacteria. Additionally, we detected an increase in transcriptome sequences of bacterial phyla Bacteriodetes, Firmicutes, Betaproteobacteria and Gammaproteobacteria-collectively presumed to be copiotrophic. Furthermore, we detected an increase in putative bacterivorous heterotrophic flagellates, likely due to predation upon the bacterial community via grazing. Although this grazing activity may explain relatively large changes in the bacterial community composition, no changes in total 16S rRNA gene copy number were observed and the total RNA level remained stable during the incubation. Together, these results are showing the first comprehensive ecological evaluation across prokaryotic and eukaryotic microbial communities on thawing and freezing of soil by application of the TotalRNA technique.

Specific recruitment of soil bacteria and fungi decomposers following a biostimulant application increased crop residues mineralization

Agriculture is undergoing important changes in order to meet sustainable soil management with respect to biodiversity (namely agroecology). Within this context, alternative solutions to mineral fertilizers such as agricultural biostimulants are thus promoted and being developed. The mechanisms by which some soil biostimulants sustain soil biological functioning and indirectly increase crop yields are still unknown. Our goal in the present study was to demonstrate if and to what extent the application of a soil biostimulant affects the soil heterotrophic microbial communities that are involved in organic matter decomposition and carbon mineralization. We hypothesized that the addition of a biostimulant results in changes in the composition and in the biomass of soil microbial communities. This in turn increases the mineralization of the organic matter derived from crop residues. We performed soil microcosm experiments with the addition of crop residues and a biostimulant, and we monitored the organic carbon (orgC) mineralization and the microbial biomass, along with the microbial community composition by sequencing 16S rRNA gene and ITS amplicons. The addition of a soil biostimulant caused a pH neutralizing effect and simultaneous enhancement of the orgC mineralization of crop residues (+ 400 μg orgC g-1 dry soil) and microbial biomass (+ 60 μg orgC g-1 dry soil) that were linked to changes in the soil microbial communities. Our findings suggest that the soil carbon mineralization enhancement in the presence of the biostimulant was supported by the specific recruitment of soil bacteria and fungi. Whereas archaea remained stable, several operational taxonomic units (OTUs) of indigenous soil bacteria and fungi were enriched and affiliated with known microbial decomposers such as Cytophagaceae, Phaselicystis sp., Verrucomicrobia, Pseudomonas sp., Ramicandelaber sp., and Mortierella sp., resulting in lower soil microbial richness and diversity.

Rapid increases in soil pH solubilise organic matter, dramatically increase denitrification potential and strongly stimulate microorganisms from the Firmicutes phylum

Rapid and transient changes in pH frequently occur in soil, impacting dissolved organic matter (DOM) and other chemical attributes such as redox and oxygen conditions. Although we have detailed knowledge on microbial adaptation to long-term pH changes, little is known about the response of soil microbial communities to rapid pH change, nor how excess DOM might affect key aspects of microbial N processing. We used potassium hydroxide (KOH) to induce a range of soil pH changes likely to be observed after livestock urine or urea fertilizer application to soil. We also focus on nitrate reductive processes by incubating microcosms under anaerobic conditions for up to 48 h. Soil pH was elevated from 4.7 to 6.7, 8.3 or 8.8, and up to 240-fold higher DOM was mobilized by KOH compared to the controls. This increased microbial metabolism but there was no correlation between DOM concentrations and CO₂ respiration nor N-metabolism rates. Microbial communities became dominated by Firmicutes bacteria within 16 h, while few changes were observed in the fungal communities. Changes in N-biogeochemistry were rapid and denitrification enzyme activity (DEA) increased up to 25-fold with the highest rates occurring in microcosms at pH 8.3 that had been incubated for 24-hour prior to measuring DEA. Nitrous oxide reductase was inactive in the pH 4.7 controls but at pH 8.3 the reduction rates exceeded 3,000 ng N₂-N g^-1 h^-1 in the presence of native DOM. Evidence for dissimilatory nitrate reduction to ammonium and/or organic matter mineralisation was observed with ammonium increasing to concentrations up to 10 times the original native soil concentrations while significant concentrations of nitrate were utilised. Pure isolates from the microcosms were dominated by Bacillus spp. and exhibited varying nitrate reductive potential.

Disentangling the complexity of permafrost soil by using high resolution profiling of microbial community composition, key functions and respiration rates

Thawing permafrost can stimulate microbial activity, leading to faster decomposition of formerly preserved organic matter and CO₂ release. Detailed knowledge about the vertical distribution of the responsible microbial community that is changing with increasing soil depth is limited. In this study, we determined the microbial community composition from cores sampled in a high Arctic heath at Svalbard, Norway; spanning from the active layer (AL) into the permafrost layer (PL). A special aim has been on identifying a layer of recently thawed soil, the transition zone (TZ), which might provide new insights into the fate of thawing permafrost. A unique sampling strategy allowed us to observe a diverse and gradually shifting microbial community in the AL, a Bacteroidetes dominated community in the TZ and throughout the PL, a community strongly dominated by a single Actinobacteria family (Intrasporangiaceae). The contrasting abundances of these two taxa caused a community difference of about 60%, just within 3 cm from TZ to PL. We incubated subsamples at about 5°C and measured highest CO₂ production rates under aerobic incubations, yet contrasting for five different layers and correlating to the microbial community composition. This high resolution strategy provides new insights on how microbial communities are structured in permafrost and a better understanding of how they respond to thaw.

The Impacts of Soil Fertility and Salinity on Soil Nitrogen Dynamics Mediated by the Soil Microbial Community Beneath the Halophytic Shrub Tamarisk

Nitrogen (N) is one of the most common limiting nutrients for primary production in terrestrial ecosystems. Soil microbes transform organic N into inorganic N, which is available to plants, but soil microbe activity in drylands is sometimes critically suppressed by environmental factors, such as low soil substrate availability or high salinity. Tamarisk (Tamarix spp.) is a halophytic shrub species that is widely distributed in the drylands of China; it produces litter enriched in nutrients and salts that are thought to increase soil fertility and salinity under its crown. To elucidate the effects of tamarisks on the soil microbial community, and thus N dynamics, by creating "islands of fertility" and "islands of salinity," we collected soil samples from under tamarisk crowns and adjacent barren areas at three habitats in the summer and fall. We analyzed soil physicochemical properties, inorganic N dynamics, and prokaryotic community abundance and composition. In soils sampled beneath tamarisks, the N mineralization rate was significantly higher, and the prokaryotic community structure was significantly different, from soils sampled in barren areas, irrespective of site and season. Tamarisks provided suitable nutrient conditions for one of the important decomposers in the area, Verrucomicrobia, by creating "islands of fertility," but provided unsuitable salinity conditions for other important decomposers, Flavobacteria, Gammaproteobacteria, and Deltaproteobacteria, by mitigating salt accumulation. However, the quantity of these decomposers tended to be higher beneath tamarisks, because they were relatively unaffected by the small salinity gradient created by the tamarisks, which may explain the higher N mineralization rate beneath tamarisks.

Linking Nitrogen Load to the Structure and Function of Wetland Soil and Rhizosphere Microbial Communities

Microorganisms living within the rhizospheres of wetland plants significantly contribute to greenhouse gas emissions. Understanding how microbes produce these gases under conditions that have been imposed by human activities (i.e., nitrogen pollution) is important to the development of future management strategies. Our results illustrate that within the rhizosphere of the wetland plant Juncus acutiflorus, physiological differences associated with nitrogen availability can influence microbial activity linked to greenhouse gas production. By pairing taxonomic information and environmental conditions like nitrogen availability with functional outputs of a system such as greenhouse gas fluxes, we present a framework to link certain taxa to both nitrogen load and greenhouse gas production. We view this type of combined information as essential in moving forward in our understanding of complex systems such as rhizosphere microbial communities.

Wetland ecosystems are important reservoirs of biodiversity and significantly contribute to emissions of the greenhouse gases CO₂, N₂O, and CH₄. High anthropogenic nitrogen (N) inputs from agriculture and fossil fuel combustion have been recognized as a severe threat to biodiversity and ecosystem functioning, such as control of greenhouse gas emissions. Therefore, it is important to understand how increased N input into pristine wetlands affects the composition and activity of microorganisms, especially in interaction with dominant wetland plants. In a series of incubations analyzed over 90 days, we disentangled the effects of N fertilization on the microbial community in bulk soil and the rhizosphere of Juncus acutiflorus, a common and abundant graminoid wetland plant. We observed an increase in greenhouse gas emissions when N is increased in incubations with J. acutiflorus, changing the system from a greenhouse gas sink to a source. Using 16S rRNA gene amplicon sequencing, we determined that the bacterial orders Opitutales, subgroup 6 Acidobacteria, and Sphingobacteriales significantly responded to high N availability. Based on metagenomic data, we hypothesize that these groups are contributing to the increased greenhouse gas emissions. These results indicated that increased N input leads to shifts in microbial activity within the rhizosphere, altering N cycling dynamics. Our study provides a framework for connecting environmental conditions of wetland bulk and rhizosphere soil to the structure and metabolic output of microbial communities.

IMPORTANCE Microorganisms living within the rhizospheres of wetland plants significantly contribute to greenhouse gas emissions. Understanding how microbes produce these gases under conditions that have been imposed by human activities (i.e., nitrogen pollution) is important to the development of future management strategies. Our results illustrate that within the rhizosphere of the wetland plant Juncus acutiflorus, physiological differences associated with nitrogen availability can influence microbial activity linked to greenhouse gas production. By pairing taxonomic information and environmental conditions like nitrogen availability with functional outputs of a system such as greenhouse gas fluxes, we present a framework to link certain taxa to both nitrogen load and greenhouse gas production. We view this type of combined information as essential in moving forward in our understanding of complex systems such as rhizosphere microbial communities.

Augmenting atrazine and hexachlorobenzene degradation under different soil redox conditions in a bioelectrochemistry system and an analysis of the relevant microorganisms

Soil microbial fuel cells (MFCs) are a sustainable technology that degrades organic pollutants while generating electricity. However, there have been no detailed studies of the mechanisms of pollutant degradation in soil MFCs. In this study, the effects of external resistance and electrode effectiveness on atrazine and hexachlorobenzene (HCB) degradation were evaluated, the performance of soil MFCs in the degradation of these pollutants under different soil redox conditions was assessed, and the associated microorganisms in the anode were investigated. With an external resistance of 20Ω, the degradation efficiencies of atrazine and HCB were 95% and 78%, respectively. The degradation efficiency, degradation rate increased with decreasing external resistance, while the half-life decreased. There were different degradation trends for different pollutants under different soil redox conditions. The fastest degradation rate of atrazine was in the upper MFC section (aerobic), whereas that of HCB was in the lower MFC section (anaerobic). The results showed that electrode effectiveness played a significant role in pollution degradation. In addition, the microbial community analysis demonstrated that Proteobacteria, especially Deltaproteobacteria involved in current generation was extremely abundant (27.49%) on soil MFC anodes, although the percentage abundances of atrazine degrading Rhodocyclaceae (8.77%), Desulfitobacterium (0.64%), and HCB degrading Desulfuromonas (0.73%), were considerably lower. The results of the study suggested that soil MFCs can enhance the degradation of atrazine and HCB, and bioelectrochemical reduction was the main mechanism for the pollutants degradation.

Comparative responses of diazotrophic abundance and community structure to the chemical composition of paddy soil

Diazotrophy is considered as one of the most crucial and dynamic phenomena in the rice field and also a major source of nitrogen input. The objective of this study was to elucidate possible interactions between diverse and dominant diazotrophic bacterial community and organic carbon composition of the paddy soil. Our results suggest that most abundantly found diazotrophs belong to a proteobacteria group and uncultured bacterial forms. A gene abundance study clearly showed significantly higher diazotrophic abundance (P < 0.01) at Chandauli (CHN) as compared to Varanasi (VNS) and Ghazipur (GHJ) districts of Eastern Uttar Pradesh, India, with nitrogenase reductase (nifH) copy number between 1.44 × 10³ and 3.34 × 10³ copy g^-1 soil. Fourier-transform infrared (FT-IR) spectroscopy data identified -CO-, C=O ([Formula: see text] and -NH-), [Formula: see text], and OH- as dominant organic functional groups in the paddy soil. Multivariate analysis was performed to get a clear and more accurate picture of interactions between free-living diazotrophs and abiotic soil factors. Regression analysis suggested a similar trend of distribution of different functional groups along each site. Relative abundance and diversity of diazotrophic population increased in response to FT-IR-based soil organic fractions. Maximum number of FT-IR spectral peak at sites in the Chandauli district augmented its bacterial diazotrophic diversity and abundance. Taken together, the present study sheds light on the substrate-driven composition of the microbial population of selected paddy areas.

Wood Ash Induced pH Changes Strongly Affect Soil Bacterial Numbers and Community Composition

Recirculation of wood ash from energy production to forest soil improves the sustainability of this energy production form as recycled wood ash contains nutrients that otherwise would be lost at harvest. In addition, wood-ash is beneficial to many soils due to its inherent acid-neutralizing capabilities. However, wood ash has several ecosystem-perturbing effects like increased soil pH and pore water electrical conductivity both known to strongly impact soil bacterial numbers and community composition. Studies investigating soil bacterial community responses to wood ash application remain sparse and the available results are ambiguous and remain at a general taxonomic level. Here we investigate the response of bacterial communities in a spruce forest soil to wood ash addition corresponding to 0, 5, 22, and 167 t wood ash ha^-1. We used culture-based enumerations of general bacteria, Pseudomonas and sporeforming bacteria combined with 16S rRNA gene amplicon sequencing to valuate soil bacterial responses to wood ash application. Results showed that wood ash addition strongly increased soil pH and electrical conductivity. Soil pH increased from acidic through neutral at 22 t ha^-1 to alkaline at 167 t ha^-1. Bacterial numbers significantly increased up to a wood ash dose of 22 t ha^-1 followed by significant decrease at 167 t ha^-1 wood ash. The soil bacterial community composition changed after wood ash application with copiotrophic bacteria responding positively up to a wood ash dose of 22 t ha^-1 while the adverse effect was seen for oligotrophic bacteria. Marked changes in bacterial community composition occurred at a wood ash dose of 167 t ha^-1 with a single alkaliphilic genus dominating. Additionally, spore-formers became abundant at an ash dose of 167 t ha^-1 whereas this was not the case at lower ash doses. Lastly, bacterial richness and diversity strongly decreased with increasing amount of wood ash applied. All of the observed bacterial responses can be directly explained by the wood ash induced changes in pH, electrical conductivity and the addition of wood ash inherent nutrients.

Dynamics of bacterial communities in rice field soils as affected by different long-term fertilization practices

Fertilization and the response of the soil microbial community to the process significantly affect crop yield and the environment. In this study, the seasonal variation in the bacterial communities in rice field soil subjected to different fertilization treatments for more than 50 years was investigated using 16S rRNA sequencing. The simultaneous application of inorganic fertilizers and rice straw compost (CAPK) maintained the species richness of the bacterial communities at levels higher than that in the case of non-fertilization (NF) and application of inorganic fertilizers only (APK) in the initial period of rice growth. The seasonal variation in the bacterial community structure in the NF and APK plots showed cyclic behavior, suggesting that the effect of season was important; however, no such trend was observed in the CAPK plot. In the CAPK plot, the relative abundances of putative copiotrophs such as Bacteroidetes, Firmicutes, and Proteobacteria were higher and those of putative oligotrophs such as Acidobacteria and Plactomycetes were lower than those in the other plots. The relative abundances of organotrophs with respiratory metabolism, such as Actinobacteria, were lower and those of chemoautotrophs that oxidize reduced iron and sulfur compounds were higher in the CAPK plot, suggesting greater carbon storage in this plot. Increased methane emission and nitrogen deficiency, which were inferred from the higher abundances of Methylocystis and Bradyrhizobium in the CAPK plot, may be a negative effect of rice straw application; thus, a solution for these should be considered to increase the use of renewable resources in agricultural lands.

Carbon Source-Dependent Effects of Anaerobic Soil Disinfestation on Soil Microbiome and Suppression of Rhizoctonia solani AG-5 and Pratylenchus penetrans

The effect of carbon source on efficacy of anaerobic soil disinfestation (ASD) toward suppression of apple root infection by Rhizoctonia solani AG-5 and Pratylenchus penetrans was examined. Orchard grass (GR), rice bran (RB), ethanol (ET), composted steer manure (CM), and Brassica juncea seed meal (SM) were used as ASD carbon inputs, with plant assays conducted in natural and pasteurized orchard soils. Subsequent studies investigated the effect of GR application rate used in ASD on control of these pathogens. In general, apple root infection by R. solani AG-5 was significantly lower in ET, GR, RB, and SM ASD treatments compared with the control. Among different ASD treatments, apple seedling growth was significantly greater when GR or SM was used as the carbon input relative to all other ASD treatments. R. solani AG-5 DNA abundance was significantly reduced in all ASD treatments, regardless of amendment type, compared with the control. In independent experiments, ASD-GR was consistently superior to ASD-CM for limiting pathogen activity in soils. ASD treatment with a grass input rate of 20 t ha(-1) provided superior suppression of P. penetrans but grass application rate did not affect ASD efficacy in control of R. solani AG-5. The soil microbiome from ASD-GR-treated soils was clearly distinct from the control and ASD-CM-treated soils. In contrast, composition of the microbiome from control and ASD-CM-treated soils could not be differentiated. Comparative results from pasteurized and nonpasteurized soils suggest that there is potential for GR based ASD treatment to recruit microbial elements that persist over the anaerobic phase of soil incubation, which may functionally contribute to disease suppression. When ASD was conducted with GR, microbial diversity was markedly reduced relative to the control or ASD-CM soil suggesting that this parameter, typically associated with system resilience, was not instrumental to the function of ASD-induced soil suppressiveness.

Biogeographic Distribution Patterns of Bacteria in Typical Chinese Forest Soils

Microbes are widely distributed in soils and play a very important role in nutrient cycling and ecosystem services. To understand the biogeographic distribution of forest soil bacteria, we collected 115 soil samples in typical forest ecosystems across eastern China to investigate their bacterial community compositions using Illumina MiSeq high throughput sequencing based on 16S rRNA. We obtained 4,667,656 sequences totally and more than 70% of these sequences were classified into five dominant groups, i.e., Actinobacteria, Acidobacteria, Alphaproteobacteria, Verrucomicrobia, and Planctomycetes (relative abundance >5%). The bacterial diversity showed a parabola shape along latitude and the maximum diversity appeared at latitudes between 33.50°N and 40°N, an area characterized by warm-temperate zones and moderate temperature, neutral soil pH and high substrate availability (soil C and N) from dominant deciduous broad-leaved forests. Pairwise dissimilarity matrix in bacterial community composition showed that bacterial community structure had regional similarity and the latitude of 30°N could be used as the dividing line between southern and northern forest soils. Soil properties and climate conditions (MAT and MAP) greatly accounted for the differences in the soil bacterial structure. Among all soil parameters determined, soil pH predominantly affected the diversity and composition of the bacterial community, and soil pH = 5 probably could be used as a threshold below which soil bacterial diversity might decline and soil bacterial community structure might change significantly. Moreover, soil exchangeable cations, especially Ca(2+) (ECa(2+)) and some other soil variables were also closely related to bacterial community structure. The selected environmental variables (21.11%) explained more of the bacterial community variation than geographic distance (15.88%), indicating that the edaphic properties and environmental factors played a more important role than geographic dispersal limitation in determining the bacterial community structure in Chinese forest soils.

The Influence of Time and Plant Species on the Composition of the Decomposing Bacterial Community in a Stream Ecosystem

Foliar chemistry influences leaf decomposition, but little is known about how litter chemistry affects the assemblage of bacterial communities during decomposition. Here we examined relationships between initial litter chemistry and the composition of the bacterial community in a stream ecosystem. We incubated replicated genotypes of Populus fremontii and P. angustifolia leaf litter that differ in percent tannin and lignin, then followed changes in bacterial community composition during 28 days of decomposition using 16S rRNA gene-based pyrosequencing. Using a nested experimental design, the majority of variation in bacterial community composition was explained by time (i.e., harvest day) (R(2) = 0.50). Plant species, nested within harvest date, explained a significant but smaller proportion of the variation (R(2) = 0.03). Significant differences in community composition between leaf species were apparent at day 14, but no significant differences existed among genotypes. Foliar chemistry correlated significantly with community composition at day 14 (r = 0.46) indicating that leaf litter with more similar phytochemistry harbor bacterial communities that are alike. Bacteroidetes and β-proteobacteria dominated the bacterial assemblage on decomposing leaves, and Verrucomicrobia and α- and δ-proteobacteria became more abundant over time. After 14 days, bacterial diversity diverged significantly between leaf litter types with fast-decomposing P. fremontii hosting greater richness than slowly decomposing P. angustifolia; however, differences were no longer present after 28 days in the stream. Leaf litter tannin, lignin, and lignin: N ratios all correlated negatively with diversity. This work shows that the bacterial community on decomposing leaves in streams changes rapidly over time, influenced by leaf species via differences in genotype-level foliar chemistry.

Pseudomonads Rule Degradation of Polyaromatic Hydrocarbons in Aerated Sediment

Given that the degradation of aromatic pollutants in anaerobic environments such as sediment is generally very slow, aeration could be an efficient bioremediation option. Using stable isotope probing (SIP) coupled with pyrosequencing analysis of 16S rRNA genes, we identified naphthalene-utilizing populations in aerated polyaromatic hydrocarbon (PAH)-polluted sediment. The results showed that naphthalene was metabolized at both 10 and 20°C following oxygen delivery, with increased degradation at 20°C as compared to 10°C—a temperature more similar to that found in situ. Naphthalene-derived ¹³C was primarily assimilated by pseudomonads. Additionally, Stenotrophomonas, Acidovorax, Comamonas, and other minor taxa were determined to incorporate ¹³C throughout the measured time course. The majority of SIP-detected bacteria were also isolated in pure cultures, which facilitated more reliable identification of naphthalene-utilizing populations as well as proper differentiation between primary consumers and cross-feeders. The pseudomonads acquiring the majority of carbon were identified as Pseudomonas veronii and Pseudomonas gessardii. Stenotrophomonads and Acidovorax defluvii, however, were identified as cross-feeders unable to directly utilize naphthalene as a growth substrate. PAH degradation assays with the isolated bacteria revealed that all pseudomonads as well as Comamonas testosteroni degraded acenaphthene, fluorene, and phenanthrene in addition to naphthalene. Furthermore, P. veronii and C. testosteroni were capable of transforming anthracene, fluoranthene, and pyrene. Screening of isolates for naphthalene dioxygenase genes using a set of in-house designed primers for Gram-negative bacteria revealed the presence of such genes in pseudomonads and C. testosteroni. Overall, our results indicated an apparent dominance of pseudomonads in the sequestration of carbon from naphthalene and potential degradation of other PAHs upon aeration of the sediment at both 20 and 10°C.

Halobacteriovorax, an underestimated predator on bacteria: potential impact relative to viruses on bacterial mortality

Predation on bacteria and accompanying mortality are important mechanisms in controlling bacterial populations and recycling of nutrients through the microbial loop. The agents most investigated and seen as responsible for bacterial mortality are viruses and protists. However, a body of evidence suggests that predatory bacteria such as the Halobacteriovorax (formerly Bacteriovorax), a Bdellovibrio-like organism, contribute substantially to bacterial death. Until now, conclusive evidence has been lacking. The goal of this study was to better understand the contributors to bacterial mortality by addressing the poorly understood role of Halobacteriovorax and how their role compares with that of viruses. The results revealed that when a concentrated suspension of Vibrio parahaemolyticus was added into microcosms of estuarine waters, the native Halobacteriovorax were the predators that responded first and most rapidly. Their numbers increased by four orders of magnitude, whereas V. parahaemolyticus prey numbers decreased by three orders of magnitude. In contrast, the extant virus population showed little increase and produced little change in the prey density. An independent experiment with stable isotope probing confirmed that Halobacteriovorax were the predators primarily responsible for the mortality of the V. parahaemolyticus. The results show that Halobacteriovorax have the potential to be significant contributors to bacterial mortality, and in such cases, predation by Halobacteriovorax may be an important mechanism of nutrient recycling. These conclusions add another dimension to bacterial mortality and the recycling of nutrients.

Patterns in species persistence and biomass production in soil microcosms recovering from a disturbance reject a neutral hypothesis for bacterial community assembly

The neutral theory of biodiversity has emerged as a major null hypothesis in community ecology. The neutral theory may sufficiently well explain the structuring of microbial communities as the extremely high microbial diversity has led to an expectation of high ecological equivalence among species. To address this possibility, we worked with microcosms of two soils; the microcosms were either exposed, or not, to a dilution disturbance which reduces community sizes and removes some very rare species. After incubation for recovery, changes in bacterial species composition in microcosms compared with the source soils were assessed by pyrosequencing of bacterial 16S rRNA genes. Our assays could detect species with a proportional abundance ≥ 0.0001 in each community, and changes in the abundances of these species should have occurred during the recovery growth, but not be caused by the disturbance per se. The undisturbed microcosms showed slight changes in bacterial species diversity and composition, with a small number of initially low-abundance species going extinct. In microcosms recovering from the disturbance, however, species diversity decreased dramatically (by > 50%); and in most cases there was not a positive relationship between species initial abundance and their chance of persistence. Furthermore, a positive relationship between species richness and community biomass was observed in microcosms of one soil, but not in those of the other soil. The results are not consistent with a neutral hypothesis that predicts a positive abundance-persistence relationship and a null effect of diversity on ecosystem functioning. Adaptation mechanisms, in particular those associated with species interactions including facilitation and predation, may provide better explanations.

Soil chemical properties affect the reaction of forest soil bacteria to drought and rewetting stress

Reaction of soil bacteria to drought and rewetting stress may depend on soil chemical properties. The objectives of this study were to test the reaction of different bacterial phyla to drought and rewetting stress and to assess the influence of different soil chemical properties on the reaction of soil bacteria to this kind of stress. The soil samples were taken at ten forest sites and measured for pH and the contents of organic C (C_org) and total N (N_t), Zn, Cu, and Pb. The samples were kept without water addition at 20 – 30 °C for 8 weeks and subsequently rewetted to achieve moisture equal to 50 – 60 % of their maximum water-holding capacity. Prior to the drought period and 24 h after the rewetting, the structure of soil bacterial communities was determined using pyrosequencing of 16S rRNA genes. The drought and rewetting stress altered bacterial community structure. Gram-positive bacterial phyla, Actinobacteria and Firmicutes, increased in relative proportion after the stress, whereas the Gram-negative bacteria in most cases decreased. The largest decrease in relative abundance was for Gammaproteobacteria and Bacteroidetes. For several phyla the reaction to drought and rewetting stress depended on the chemical properties of soils. Soil pH was the most important soil property influencing the reaction of a number of soil bacterial groups (including all classes of Proteobacteria, Bacteroidetes, Acidobacteria, and others) to drought and rewetting stress. For several bacterial phyla the reaction to the stress depended also on the contents of N_t and C_org in soil. The effect of heavy metal pollution was also noticeable, although weaker compared to other chemical soil properties. We conclude that soil chemical properties should be considered when assessing the effect of stressing factors on soil bacterial communities.

Field-scale tracking of active methane-oxidizing communities in a landfill cover soil reveals spatial and seasonal variability

Aerobic methane-oxidizing bacteria (MOB) in soils mitigate methane (CH4 ) emissions. We assessed spatial and seasonal differences in active MOB communities in a landfill cover soil characterized by highly variable environmental conditions. Field-based measurements of CH4 oxidation activity and stable-isotope probing of polar lipid-derived fatty acids (PLFA-SIP) were complemented by microarray analysis of pmoA genes and transcripts, linking diversity and function at the field scale. In situ CH4 oxidation rates varied between sites and were generally one order of magnitude lower in winter compared with summer. Results from PLFA-SIP and pmoA transcripts were largely congruent, revealing distinct spatial and seasonal clustering. Overall, active MOB communities were highly diverse. Type Ia MOB, specifically Methylomonas and Methylobacter, were key drivers for CH4 oxidation, particularly at a high-activity site. Type II MOB were mainly active at a site showing substantial fluctuations in CH4 loading and soil moisture content. Notably, Upland Soil Cluster-gamma-related pmoA transcripts were also detected, indicating concurrent oxidation of atmospheric CH4 . Spatial separation was less distinct in winter, with Methylobacter and uncultured MOB mediating CH4 oxidation. We propose that high diversity of active MOB communities in this soil is promoted by high variability in environmental conditions, facilitating substantial removal of CH4 generated in the waste body.

Stable isotope probing to study functional components of complex microbial ecosystems

This protocol presents a method of dissecting the DNA or RNA of key organisms involved in a specific biochemical process within a complex ecosystem. Stable isotope probing (SIP) allows the labelling and separation of nucleic acids from community members that are involved in important biochemical transformations, yet are often not the most numerically abundant members of a community. This pure culture-independent technique circumvents limitations of traditional microbial isolation techniques or data mining from large-scale whole-community metagenomic studies to tease out the identities and genomic repertoires of microorganisms participating in biological nutrient cycles. SIP experiments can be applied to virtually any ecosystem and biochemical pathway under investigation provided a suitable stable isotope substrate is available. This versatile methodology allows a wide range of analyses to be performed, from fatty-acid analyses, community structure and ecology studies, and targeted metagenomics involving nucleic acid sequencing. SIP experiments provide an effective alternative to large-scale whole-community metagenomic studies by specifically targeting the organisms or biochemical transformations of interest, thereby reducing the sequencing effort and time-consuming bioinformatics analyses of large datasets.

Bacterial acquisition of hexachlorobenzene-derived carbon in contaminated soil

Pesticides are a class of xenobiotics intentionally released into the environment. Hexachlorobenzene (HCB) was used as a fungicide from 1945, leaving behind many contaminated sites. Very few studies have examined the biodegradation of HCB or the fate of HCB-derived carbon. Here we report that certain bacterial populations are capable of deriving carbon from HCB in contaminated soil under aerobic conditions. These populations are primarily Proteobacteria, including Methylobacterium and Pseudomonas, which predominated as detected by stable isotope probing (SIP) and 16S rRNA gene amplicon pyrosequencing. Due to the nature of SIP, which can be used as a functional method solely for assimilatory processes, it is not possible to elucidate whether these populations metabolized directly HCB or intermediates of its metabolism produced by different populations. The possibility exists that HCB is degraded via the formation of pentachlorophenol (PCP), which is further mineralized. With this in mind, we designed primers to amplify PCP 4-monooxygenase-coding sequences based on the available pcpB gene sequence from Methylobacterium radiotolerans JCM 2831. Based on 16S rRNA gene analysis, organisms closely related to this strain were detected in (13)C-labeled DNA. Using the designed primers, we were able to amplify pcpB genes in both total community DNA and (13)C-DNA. This indicates that HCB might be transformed into PCP before it gets assimilated. In summary, this study is the first report on which bacterial populations benefit from carbon originating in the pesticide HCB in a contaminated soil.

Importance of soil organic matter for the diversity of microorganisms involved in the degradation of organic pollutants

Many organic pollutants are readily degradable by microorganisms in soil, but the importance of soil organic matter for their transformation by specific microbial taxa is unknown. In this study, sorption and microbial degradation of phenol and 2,4-dichlorophenol (DCP) were characterized in three soil variants, generated by different long-term fertilization regimes. Compared with a non-fertilized control (NIL), a mineral-fertilized NPK variant showed 19% and a farmyard manure treated FYM variant 46% more soil organic carbon (SOC). Phenol sorption declined with overall increasing SOC because of altered affinities to the clay fraction (soil particles <2 mm in diameter). In contrast, DCP sorption correlated positively with particulate soil organic matter (present in the soil particle fractions of 63-2000 μm). Stable isotope probing identified Rhodococcus, Arthrobacter (both Actinobacteria) and Cryptococcus (Basidiomycota) as the main degraders of phenol. Rhodococcus and Cryptococcus were not affected by SOC, but the participation of Arthrobacter declined in NPK and even more in FYM. (14)C-DCP was hardly metabolized in the NIL variant, more efficiently in FYM and most in NPK. In NPK, Burkholderia was the main degrader and in FYM Variovorax. This study demonstrates a strong effect of SOC on the partitioning of organic pollutants to soil particle size fractions and indicates the profound consequences that this process could have for the diversity of bacteria involved in their degradation.

Soil microbial communities respond differently to three chemically defined polyphenols

High molecular weight polyphenols (e.g. tannins) that enter the soil may affect microbial populations, by serving as substrates for microbial respiration or by selecting for certain microbes. In this study we examined how three phenolic compounds that represent some environmentally widespread tannins or their constituent functional groups were respired by soil microorganisms and how the compounds affected the abundance and diversity of soil bacteria and archaea, including ammonia oxidizers. An acidic, silt loam soil from a pine forest was incubated for two weeks with the monomeric phenol methyl gallate, the small polyphenol epigallocatechin gallate, or the large polyphenol oenothein B. Respiration of the polyphenols during the incubation was measured using the Microresp™ system. After incubation, metabolic diversity was determined by community level physiological profiling (CLPP), and genetic diversity was determined using denaturing gradient gel electrophoresis (DGGE) analysis on DNA extracted from the soil samples. Total microbial populations and ammonia-oxidizing populations were measured using real time quantitative polymerase chain reaction (qPCR). Methyl gallate was respired more efficiently than the higher molecular weight tannins but not as efficiently as glucose. Methyl gallate and epigallocatechin gallate selected for genetically or physiologically unique populations compared to glucose. None of the polyphenols supported microbial growth, and none of the polyphenols affected ammonia-oxidizing bacterial populations or ammonia-oxidizing archaea. Additional studies using both a wider range of polyphenols and a wider range of soils and environments are needed to elucidate the role of polyphenols in determining soil microbiological diversity.

Microbial syntrophy: interaction for the common good

Classical definitions of syntrophy focus on a process, performed through metabolic interaction between dependent microbial partners, such as the degradation of complex organic compounds under anoxic conditions. However, examples from past and current scientific discoveries suggest that a new, simple but wider definition is necessary to cover all aspects of microbial syntrophy. We suggest the term 'obligately mutualistic metabolism', which still focuses on microbial metabolic cooperation but also includes an ecological aspect: the benefit for both partners. By the combined metabolic activity of microorganisms, endergonic reactions can become exergonic through the efficient removal of products and therefore enable a microbial community to survive with minimal energy resources. Here, we explain the principles of classical and non-classical syntrophy and illustrate the concepts with various examples. We present biochemical fundamentals that allow microorganism to survive under a range of environmental conditions and to drive important biogeochemical processes. Novel technologies have contributed to the understanding of syntrophic relationships in cultured and uncultured systems. Recent research highlights that obligately mutualistic metabolism is not limited to certain metabolic pathways nor to certain environments or microorganisms. This beneficial microbial interaction is not restricted to the transfer of reducing agents such as hydrogen or formate, but can also involve the exchange of organic, sulfurous- and nitrogenous compounds or the removal of toxic compounds.

Bacterial genome replication at subzero temperatures in permafrost

Microbial metabolic activity occurs at subzero temperatures in permafrost, an environment representing ∼25% of the global soil organic matter. Although much of the observed subzero microbial activity may be due to basal metabolism or macromolecular repair, there is also ample evidence for cellular growth. Unfortunately, most metabolic measurements or culture-based laboratory experiments cannot elucidate the specific microorganisms responsible for metabolic activities in native permafrost, nor, can bulk approaches determine whether different members of the microbial community modulate their responses as a function of changing subzero temperatures. Here, we report on the use of stable isotope probing with (13)C-acetate to demonstrate bacterial genome replication in Alaskan permafrost at temperatures of 0 to -20 °C. We found that the majority (80%) of operational taxonomic units detected in permafrost microcosms were active and could synthesize (13)C-labeled DNA when supplemented with (13)C-acetate at temperatures of 0 to -20 °C during a 6-month incubation. The data indicated that some members of the bacterial community were active across all of the experimental temperatures, whereas many others only synthesized DNA within a narrow subzero temperature range. Phylogenetic analysis of (13)C-labeled 16S rRNA genes revealed that the subzero active bacteria were members of the Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes and Proteobacteria phyla and were distantly related to currently cultivated psychrophiles. These results imply that small subzero temperature changes may lead to changes in the active microbial community, which could have consequences for biogeochemical cycling in permanently frozen systems.

Diversity of planktonic and attached bacterial communities in a phenol-contaminated sandstone aquifer

Polluted aquifers contain indigenous microbial communities with the potential for in situ bioremediation. However, the effect of hydrogeochemical gradients on in situ microbial communities (especially at the plume fringe, where natural attenuation is higher) is still not clear. In this study, we used culture-independent techniques to investigate the diversity of in situ planktonic and attached bacterial communities in a phenol-contaminated sandstone aquifer. Within the upper and lower plume fringes, denaturing gradient gel electrophoresis profiles indicated that planktonic community structure was influenced by the steep hydrogeochemical gradient of the plume rather than the spatial location in the aquifer. Under the same hydrogeochemical conditions (in the lower plume fringe, 30 m below ground level), 16S rRNA gene cloning and sequencing showed that planktonic and attached bacterial communities differed markedly and that the attached community was more diverse. The 16S rRNA gene phylogeny also suggested that a phylogenetically diverse bacterial community operated at this depth (30 mbgl), with biodegradation of phenolic compounds by nitrate-reducing Azoarcus and Acidovorax strains potentially being an important process. The presence of acetogenic and sulphate-reducing bacteria only in the planktonic clone library indicates that some natural attenuation processes may occur preferentially in one of the two growth phases (attached or planktonic). Therefore, this study has provided a better understanding of the microbial ecology of this phenol-contaminated aquifer, and it highlights the need for investigating both planktonic and attached microbial communities when assessing the potential for natural attenuation in contaminated aquifers.

Substrate removal and electricity generation in a membrane-less microbial fuel cell for biological treatment of wastewater

Microbial fuel cells have gained popularity in recent years due to its promise in converting organic wastewater into renewable electrical energy. In this study, a membrane-less MFC with a biocathode was developed to evaluate its performance in electricity generation while simultaneously treating wastewater. The MFC fed with a continuous flow of 2g/day acetate produced a power density of 30 mW/m(2) and current density of 245 mA/m(2). A substrate degradation efficiency (SDE) of 75.9% was achieved with 48.7% attributed to the anaerobic process and 27.2% to the aerobic process. Sequencing analysis of the microbial consortia using 16S rDNA pryosequencing showed the predominance of Bacteroidia in the anode after one month of operation, while the microbial community in the cathode chamber was dominated by Gamma-proteobacteria and Beta-proteobacteria. Coulombic efficiencies varied from 19.8% to 58.1% using different acetate concentrations, indicating power density can be further improved through the accumulation of electron-transferring bacteria.

Identification of biomass utilizing bacteria in a carbon-depleted glacier forefield soil by the use of 13C DNA stable isotope probing

As Alpine glaciers are retreating rapidly, bare soils with low organic C and N contents are becoming exposed. Carbon availability is a key factor regulating microbial diversity and ecosystem functioning in these soils. The aim of this study was to investigate how bacterial activity, community structure and composition are influenced by organic carbon availability. Bare soils were supplied with (13)C-labelled fungal (Penicillium sp.) and green algal (Chlorella sp.) biomass and the CO2 evolution and its δ(13)C signature were monitored up to 60 days. These organisms have previously been isolated near the glacier terminus. DNA stable isotope probing followed by T-RFLP profiling and sequencing of 16S rRNA genes was employed to identify consumers able to assimilate carbon from these biomass amendments. Higher respiration and higher bacterial activity indicated a more efficient utilization of algal cells than fungal cells. Flavobacterium sp. predominantly incorporated fungal-derived C, whereas the algal-derived C was mainly incorporated by Acidobacteria and Proteobacteria. This study emphasizes the important role of both fungal and algal biomass in increasing the carbon pool in recently deglaciated bare soils, as only 20% of the added C was respired as CO2, and the rest, we presume, remained in the soil.