Change in gene abundance in the nitrogen biogeochemical cycle with temperature and nitrogen addition in Antarctic soils

Temporal and Spatial Dynamics of Archaeal Communities in Two Freshwater Lakes at Different Trophic Status

In either eutrophic Dianchi Lake or mesotrophic Erhai Lake, the abundance, diversity, and structure of archaeaplankton communities in spring were different from those in summer. In summer, archaeaplankton abundance generally decreased in Dianchi Lake but increased in Erhai Lake, while archaeaplankton diversity increased in both lakes. These two lakes had distinct archaeaplankton community structure. Archaeaplankton abundance was influenced by organic content, while trophic status determined archaeaplankton diversity and structure. Moreover, in summer, lake sediment archaeal abundance considerably decreased. Sediment archaeal abundance showed a remarkable spatial change in spring but only a slight one in summer. The evident spatial change of sediment archaeal diversity occurred in both seasons. In Dianchi Lake, sediment archaeal community structure in summer was remarkably different from that in spring. Compared to Erhai Lake, Dianchi Lake had relatively high sediment archaeal abundance but low diversity. These two lakes differed remarkably in sediment archaeal community structure. Trophic status determined sediment archaeal abundance, diversity and structure. Archaeal diversity in sediment was much higher than that in water. Water and sediment habitats differed greatly in archaeal community structure. Euryarchaeota predominated in water column, but showed much lower proportion in sediment. Bathyarchaeota was an important component of sediment archaeal community.

Metagenomic and functional analyses of the consequences of reduction of bacterial diversity on soil functions and bioremediation in diesel-contaminated microcosms

The relationship between microbial biodiversity and soil function is an important issue in ecology, yet most studies have been performed in pristine ecosystems. Here, we assess the role of microbial diversity in ecological function and remediation strategies in diesel-contaminated soils. Soil microbial diversity was manipulated using a removal by dilution approach and microbial functions were determined using both metagenomic analyses and enzymatic assays. A shift from Proteobacteria- to Actinobacteria-dominant communities was observed when species diversity was reduced. Metagenomic analysis showed that a large proportion of functional gene categories were significantly altered by the reduction in biodiversity. The abundance of genes related to the nitrogen cycle was significantly reduced in the low-diversity community, impairing denitrification. In contrast, the efficiency of diesel biodegradation was increased in the low-diversity community and was further enhanced by addition of red clay as a stimulating agent. Our results suggest that the relationship between microbial diversity and ecological function involves trade-offs among ecological processes, and should not be generalized as a positive, neutral, or negative relationship.

Microbial diversity and functional capacity in polar soils

Global change is disproportionately affecting cold environments (polar and high elevation regions), with potentially negative impacts on microbial diversity and functional processes. In most cold environments the combination of low temperatures, and physical stressors, such as katabatic wind episodes and limited water availability result in biotic systems, which are in trophic terms very simple and primarily driven by microbial communities. Metagenomic approaches have provided key insights on microbial communities in these systems and how they may adapt to stressors and contribute towards mediating crucial biogeochemical cycles. Here we review, the current knowledge regarding edaphic-based microbial diversity and functional processes in Antarctica, and the Artic. Such insights are crucial and help to establish a baseline for understanding the impact of climate change on Polar Regions.

Nanoparticles Based on Chitosan as Carriers for the Combined Herbicides Imazapic and Imazapyr

The use of lower concentrations and fewer applications of herbicides is one of the prime objectives of the sustainable agriculture as it decreases the toxicity to non-targeted organisms and the risk of wider environmental contamination. In the present work, nanoparticles were developed for encapsulation of the herbicides imazapic and imazapyr. Alginate/chitosan and chitosan/tripolyphosphate nanoparticles were manufactured, and their physicochemical stability was evaluated. Determinations were made of the encapsulation efficiency and release kinetics, and the toxicity of the nanoparticles was evaluated using cytotoxicity and genotoxicity assays. The effects of herbicides and herbicide-loaded nanoparticles on soil microorganisms were studied in detail using real-time polymerase chain reactions. The nanoparticles showed an average size of 400 nm and remained stable during 30 days of storage at ambient temperature. Satisfactory encapsulation efficiencies of between 50 and 70% were achieved for both types of particles. Cytotoxicity assays showed that the encapsulated herbicides were less toxic, compared to the free compounds, and genotoxicity was decreased. Analyses of soil microbiota revealed changes in the bacteria of the soils exposed to the different treatments. Our study proves that encapsulation of the herbicides improved their mode of action and reduced their toxicity, indicating their suitability for use in future practical applications.

Spatiotemporal variation of planktonic and sediment bacterial assemblages in two plateau freshwater lakes at different trophic status

Both planktonic and sediment bacterial assemblages are the important components of freshwater lake ecosystems. However, their spatiotemporal shift and the driving forces remain still elusive. Eutrotrophic Dianchi Lake and mesotrophic Erhai Lake are the largest two freshwater lakes on the Yunnan Plateau (southwestern China). The present study investigated the spatiotemporal shift in both planktonic and sediment bacterial populations in these two plateau freshwater lakes at different trophic status. For either lake, both water and sediment samples were collected from six sampling locations in spring and summer. Bacterioplankton community abundance in Dianchi Lake generally far outnumbered that in Erhai Lake. Sediment bacterial communities in Erhai Lake were found to have higher richness and diversity than those in Dianchi Lake. Sediments had higher bacterial community richness and diversity than waters. The change patterns for both planktonic and sediment bacterial communities were lake-specific and season-specific. Either planktonic or sediment bacterial community structure showed a distinct difference between in Dianchi Lake and in Erhai Lake, and an evident structure difference was also found between planktonic and sediment bacterial communities in either of these two lakes. Planktonic bacterial communities in both Dianchi Lake and Erhai Lake mainly included Proteobacteria (mainly Alpha-, Beta-, and Gammaproteobacteria), Bacteroidetes, Actinobacteria, Cyanobacteria, and Firmicutes, while sediment bacterial communities were mainly represented by Proteobacteria (mainly Beta- and Deltaproteobacteria), Bacteroidetes, Chlorobi, Nitrospirae, Acidobacteria, and Chloroflexi. Trophic status could play important roles in shaping both planktonic and sediment bacterial communities in freshwater lakes.

Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils

Increasing temperatures have been shown to impact soil biogeochemical processes, although the corresponding changes to the underlying microbial functional communities are not well understood. Alterations in the nitrogen (N) cycling functional component are particularly important as N availability can affect microbial decomposition rates of soil organic matter and influence plant productivity. To assess changes in the microbial component responsible for these changes, the composition of the N-fixing (nifH), and denitrifying (nirS, nirK, nosZ) soil microbial communities was assessed by targeted pyrosequencing of functional genes involved in N cycling in two major biomes where the experimental effect of climate warming is under investigation, a tallgrass prairie in Oklahoma (OK) and the active layer above permafrost in Alaska (AK). Raw reads were processed for quality, translated with frameshift correction, and a total of 313,842 amino acid sequences were clustered and linked to a nearest neighbor using reference datasets. The number of OTUs recovered ranged from 231 (NifH) to 862 (NirK). The N functional microbial communities of the prairie, which had experienced a decade of experimental warming were the most affected with changes in the richness and/or overall structure of NifH, NirS, NirK and NosZ. In contrast, the AK permafrost communities, which had experienced only 1 year of warming, showed decreased richness and a structural change only with the nirK-harboring bacterial community. A highly divergent nirK-harboring bacterial community was identified in the permafrost soils, suggesting much novelty, while other N functional communities exhibited similar relatedness to the reference databases, regardless of site. Prairie and permafrost soils also harbored highly divergent communities due mostly to differing major populations.

Sequential decolorization of azo dye and mineralization of decolorization liquid coupled with bioelectricity generation using a pH self-neutralized photobioelectrochemical system operated with polarity reversion

A novel photobioelectrochemical system (PBES) was developed by acclimating algal-bacterial biofilm in both anode and cathode using Chlorella vulgaris and indigenous wastewater bacteria as inoculums. The PBES was operated in polarity reversion mode depend on dark/light alternate reaction to achieve simultaneous pH self-neutralization, azo dye degradation (Congo red) and bioelectricity generation. The anodic accumulated acidity and cathodic accumulated alkalinity were self-neutralized after polarity reversion and hence eliminate the membrane pH gradient. The Congo red was first decolored in the dark anode and the resultant decolorization liquid was subsequently mineralized after the dark anode changing to the photo-biocathode. The presence of C. vulgaris significantly enhanced the two-stage degradation of Congo red, with 93% increases in decolorization rates and 8% increases in mineralization compared to the algae-free BES. The PBES continuously generated stable voltage output over four months under repeatedly reversion of polarity. The maximum power density produced before and after polarity reversion was 78 and 61 mW/m(2), respectively. The synergy between C. vulgaris and mixed bacteria was responsible for the successful operation of the PBES which can be potentially applied to treat wastewater containing azo dye with benefits of enhanced azo dye degradation, high net power output and buffer minimization.

Effects of seasonal temperature variation on nitrification, anammox process, and bacteria involved in a pilot-scale constructed wetland

Effects of seasonal temperature (especially low temperature) variation on nitrogen removal process and bacteria involved in an experimental domestic wastewater treatment wetland were investigated in this study. Three different functional groups of bacteria, namely anammox bacteria, ammonia-oxidizing bacteria (AOB), and Nitrospira sp., were involved. Anammox process was seriously inhibited with mean temperature lower than 15 °C. However, obvious adaptation of anammox bacteria also appeared after a long time operation under low temperatures. Contrary to anammox bacteria, AOB were more abundant in winter than in summer. Nitrospira sp. was the least prevalent and showed the lowest level of variation. Distinct nitrate accumulation observed under winter temperatures was likely due to inhibition of anammox process, comparative advantage of Nitrospira sp. in winter, and the presence of cold-tolerant AOB species.

Distribution of sediment bacterial and archaeal communities in plateau freshwater lakes

Both Bacteria and Archaea might be involved in various biogeochemical processes in lacustrine sediment ecosystems. However, the factors governing the intra-lake distribution of sediment bacterial and archaeal communities in various freshwater lakes remain unclear. The present study investigated the sediment bacterial and archaeal communities in 13 freshwater lakes on the Yunnan Plateau. Quantitative PCR assay showed a large variation in bacterial and archaeal abundances. Illumina MiSeq sequencing illustrated high bacterial and archaeal diversities. Bacterial abundance was regulated by sediment total organic carbon and total nitrogen, and water depth, while nitrate nitrogen was an important determinant of bacterial diversity. Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, and Verrucomicrobia were the major components of sediment bacterial communities. Proteobacteria was the largest phylum, but its major classes and their proportions varied greatly among different lakes, affected by sediment nitrate nitrogen. In addition, both Euryarchaeota and Crenarchaeota were important members in sediment archaeal communities, while unclassified Archaea usually showed the dominance.

Influence of soil properties on archaeal diversity and distribution in the McMurdo Dry Valleys, Antarctica

Archaea are the least understood members of the microbial community in Antarctic mineral soils. Although their occurrence in Antarctic coastal soils has been previously documented, little is known about their distribution in soils across the McMurdo Dry Valleys, Victoria Land. In this study, terminal-restriction fragment length polymorphism (t-RFLP) analysis and 454 pyrosequencing were coupled with a detailed analysis of soil physicochemical properties to characterize archaeal diversity and identify environmental factors that might shape and maintain archaeal communities in soils of the three southern most McMurdo Dry Valleys (Garwood, Marshall, and Miers Valley). Archaea were successfully detected in all inland and coastal mineral soils tested, revealing a low overall richness (mean of six operational taxonomic units [OTUs] per sample site). However, OTU richness was higher in some soils and this higher richness was positively correlated with soil water content, indicating water as a main driver of archaeal community richness. In total, 18 archaeal OTUs were detected, predominately Thaumarchaeota affiliated with Marine Group 1.1b (> 80% of all archaeal sequences recovered). Less abundant OTUs (2% of all archaeal sequences) were loosely related to members of the phylum Euryarchaeota. This is the first comprehensive study showing a widespread presence and distribution of Archaea in inland Antarctic soils.

Microbial ecology and biogeochemistry of continental Antarctic soils

The Antarctica Dry Valleys are regarded as the coldest hyperarid desert system on Earth. While a wide variety of environmental stressors including very low minimum temperatures, frequent freeze-thaw cycles and low water availability impose severe limitations to life, suitable niches for abundant microbial colonization exist. Antarctic desert soils contain much higher levels of microbial diversity than previously thought. Edaphic niches, including cryptic and refuge habitats, microbial mats and permafrost soils all harbor microbial communities which drive key biogeochemical cycling processes. For example, lithobionts (hypoliths and endoliths) possess a genetic capacity for nitrogen and carbon cycling, polymer degradation, and other system processes. Nitrogen fixation rates of hypoliths, as assessed through acetylene reduction assays, suggest that these communities are a significant input source for nitrogen into these oligotrophic soils. Here we review aspects of microbial diversity in Antarctic soils with an emphasis on functionality and capacity. We assess current knowledge regarding adaptations to Antarctic soil environments and highlight the current threats to Antarctic desert soil communities.

Depth-related changes of sediment ammonia-oxidizing microorganisms in a high-altitude freshwater wetland

Both ammonia-oxidizing bacteria (AOB) and archaea (AOA) might be the key microorganisms in ammonia conversion in ecosystems. However, the depth-related change of AOA and AOB in sediment ecosystem is still not clear. The relative contribution of AOA and AOB to nitrification in wetland sediment remains also unclear. Moreover, information about ammonia-oxidizing microorganisms in high-altitude freshwater wetland is still lacking. The present study investigated the relative abundances and community structures of AOA and AOB in sediments of a high-altitude freshwater wetland in Yunnan Province (China). Variations of the relative abundances and community structures of AOA and AOB were found in the wetland sediments, dependent on both sampling site and sediment depth. The relative abundances of AOA and AOB (0.04-3.84 and 0.01-0.52 %) and the AOA/AOB ratio (0.12-4.65) showed different depth-related change patterns. AOB community size was usually larger than AOA community size. AOB diversity was usually higher than AOA diversity. AOA diversity decreased with the increase of sediment depth, while AOB diversity showed no obvious link with the sediment depth. Pearson's correlation analysis showed that AOA diversity had a positive significant correlation with available phosphorus. Nitrosospira-like sequences, with different compositions, predominated in the wetland sediment AOB communities. This work could provide some new insights toward nitrification in freshwater sediment ecosystems.

Nitrite reductase genes as functional markers to investigate diversity of denitrifying bacteria during agricultural waste composting

The purpose of this study was to investigate the diversity of denitrifier community during agricultural waste composting. The diversity and dynamics of the denitrifying genes (nirK and nirS) were determined using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Relationships between physico-chemical parameters and denitrifying genes structures were simultaneously evaluated by redundancy analysis (RDA). Phylogenetic analysis indicated that nirK clones grouped into six clusters and nirS clones into two major clusters, respectively. The results showed a very high diversity of nir gene sequences within composting samples. RDA showed that the nirK and nirS gene structures were significantly related to pH and pile temperature (P < 0.05). Significant amounts of the variation (49.2 and 38.3 % for nirK and nirS genes, respectively) were explained by pH and pile temperature, suggesting that those two parameters were the most likely ones to influence, or be influenced by the denitrifiers harboring nirK and nirS genes.

Vascular plants mediate the effects of aridity and soil properties on ammonia-oxidizing bacteria and archaea

An integrated perspective of the most important factors driving the abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in natural ecosystems is lacking, especially in drylands. We evaluated how different climatic, abiotic, and nutrient-related factors determine AOA and AOB abundance in bare and vegetated microsites from grasslands throughout the Mediterranean Basin. We found a strong negative relationship between the abundance of AOA genes and soil fertility (availability of C, N, and P). Aridity and other abiotic factors (pH, sand content, and electrical conductivity) were more important than soil fertility in modulating the AOA/AOB ratio. AOB were more abundant under vegetated microsites, while AOA, highly resistant to stressful conditions, were more abundant in bare ground areas. These results suggest that AOA may carry out nitrification in less fertile microsites, while AOB predominate under more fertile conditions. Our results indicate that the influence of aridity and pH on the relative dominance of AOA and AOB genes is ultimately determined by local-scale environmental changes promoted by perennial vegetation. Thus, in spatially heterogeneous ecosystems such as drylands, there is a mutual exclusion and niche division between these microorganisms, suggesting that they may be functionally complementary.

Spatial and temporal variation of archaeal, bacterial and fungal communities in agricultural soils

BACKGROUND

Soil microbial communities are in constant change at many different temporal and spatial scales. However, the importance of these changes to the turnover of the soil microbial communities has been rarely studied simultaneously in space and time.

METHODOLOGY/PRINCIPAL FINDINGS

In this study, we explored the temporal and spatial responses of soil bacterial, archaeal and fungal β-diversities to abiotic parameters. Taking into account data from a 3-year sampling period, we analyzed the abundances and community structures of Archaea, Bacteria and Fungi along with key soil chemical parameters. We questioned how these abiotic variables influence the turnover of bacterial, archaeal and fungal communities and how they impact the long-term patterns of changes of the aforementioned soil communities. Interestingly, we found that the bacterial and fungal β-diversities are quite stable over time, whereas archaeal diversity showed significantly higher fluctuations. These fluctuations were reflected in temporal turnover caused by soil management through addition of N-fertilizers.

CONCLUSIONS

Our study showed that management practices applied to agricultural soils might not significantly affect the bacterial and fungal communities, but cause slow and long-term changes in the abundance and structure of the archaeal community. Moreover, the results suggest that, to different extents, abiotic and biotic factors determine the community assembly of archaeal, bacterial and fungal communities.

Primers for amplification of nitrous oxide reductase genes associated with Firmicutes and Bacteroidetes in organic-compound-rich soils

The nosZ gene encodes nitrous oxide reductase, a key enzyme in the nitrous oxide reduction that occurs during complete denitrification. Many conventional approaches have used Proteobacteria-based primers to detect nosZ in environmental samples. However, these primers often fail to detect nosZ in non-Proteobacteria strains, including Firmicutes (Gram-positive) and Bacteroidetes. In this study, newly designed nosZ primers successfully amplified this gene from five Geobacillus species (Firmicutes). The primers were used to construct nosZ clone libraries from DNA extracted from sludge and domestic animal feedlot soils, all with high organic carbon contents. After DNA sequencing, phylogenetic analysis identified many new nosZ sequences with high levels of homology to nosZ from Bacteroidetes, probably because of the high sequence similarity of nosZ from Firmicutes and Bacteroidetes, and a predominance of Bacteroidetes in feedlot environments. Three sets of new quantitative real-time PCR (qPCR) primers based on our clone library sequences were designed and tested for their specificities. Our data showed that only Bacteroidetes-related nosZ sequences were amplified, whereas conventional Proteobacteria-based primers amplified only Proteobacteria-related nosZ. Quantitative analysis of nosZ with the new qPCR primers recovered ~10(4) copies per 100 ng DNA. Thus, it appears that amplification with conventional primers is insufficient for developing an understanding of the diversity and abundance of nosZ genes in the environment.

Archaeal dominated ammonia-oxidizing communities in Icelandic grassland soils are moderately affected by long-term N fertilization and geothermal heating

The contribution of ammonia-oxidizing bacteria and archaea (AOB and AOA, respectively) to the net oxidation of ammonia varies greatly between terrestrial environments. To better understand, predict and possibly manage terrestrial nitrogen turnover, we need to develop a conceptual understanding of ammonia oxidation as a function of environmental conditions including the ecophysiology of associated organisms. We examined the discrete and combined effects of mineral nitrogen deposition and geothermal heating on ammonia-oxidizing communities by sampling soils from a long-term fertilization site along a temperature gradient in Icelandic grasslands. Microarray, clone library and quantitative PCR analyses of the ammonia monooxygenase subunit A (amoA) gene accompanied by physico-chemical measurements of the soil properties were conducted. In contrast to most other terrestrial environments, the ammonia-oxidizing communities consisted almost exclusively of archaea. Their bacterial counterparts proved to be undetectable by quantitative polymerase chain reaction suggesting AOB are only of minor relevance for ammonia oxidation in these soils. Our results show that fertilization and local, geothermal warming affected detectable ammonia-oxidizing communities, but not soil chemistry: only a subset of the detected AOA phylotypes was present in higher temperature soils and AOA abundance was increased in the fertilized soils, while soil physio-chemical properties remained unchanged. Differences in distribution and structure of AOA communities were best explained by soil pH and clay content irrespective of temperature or fertilizer treatment in these grassland soils, suggesting that these factors have a greater potential for ecological niche-differentiation of AOA in soil than temperature and N fertilization.

Effects of temperatures near the freezing point on N2O emissions, denitrification and on the abundance and structure of nitrifying and denitrifying soil communities

Climate warming in temperate regions may lead to decreased soil temperatures over winter as a result of reduced snow cover. We examined the effects of temperatures near the freezing point on N(2)O emissions, denitrification, and on the abundance and structure of soil nitrifiers and denitrifiers. Soil microcosms supplemented with NO3 - and/or NO3 - plus red clover residues were incubated for 120 days at -4 °C, -1 °C, +2 °C or +5 °C. Among microcosms amended with residues, N(2)O emission and/or denitrification increased with increasing temperature on Days 2 and 14. Interestingly, N(2)O emission and/or denitrification after Day 14 were the greatest at -1 °C. Substantial N(2) O emissions were only observed on Day 2 at +2 °C and +5 °C, while at -1 °C, N(2)O emissions were consistently detected over the duration of the experiment. Abundances of ammonia oxidizing bacteria (AOB) and archaea (AOA), Nitrospira-like bacteria and nirK denitrifiers were the lowest in soils at -4 °C, while abundances of Nitrobacter-like bacteria and nirS denitrifiers did not vary among temperatures. Community structures of nirK and nirS denitrifiers and Nitrobacter-like bacteria shifted between below-zero and above-zero temperatures. Structure of AOA and AOB communities also changed but not systematically among frozen and unfrozen temperatures. Results indicated shifts in some nitrifier and denitrifier communities with freezing and a surprising stimulation of N(2)O emissions at -1 °C when NO3 - and C are present.

Seasonal changes in nitrogen-cycle gene abundances and in bacterial communities in acidic forest soils

The abundance of genes related to the nitrogen biogeochemical cycle and the microbial community in forest soils (bacteria, archaea, fungi) were quantitatively analyzed via real-time PCR using 11 sets of specific primers amplifying nifH, bacterial amoA, archaeal amoA, narG, nirS, nirK, norB, nosZ, bacterial 16S rRNA gene, archaeal 16S rRNA gene, and the ITS sequence of fungi. Soils were sampled from Bukhan Mountain from September of 2010 to July of 2011 (7 times). Bacteria were the predominant microbial community in all samples. However, the abundance of archaeal amoA was greater than bacterial amoA throughout the year. The abundances of nifH, nirS, nirK, and norB genes changed in a similar pattern, while narG and nosZ appeared in sensitive to the environmental changes. Clone libraries of bacterial 16S rRNA genes were constructed from summer and winter soil samples and these revealed that Acidobacteria was the most predominant phylum in acidic forest soil environments in both samples. Although a specific correlation of environmental factor and gene abundance was not verified by principle component analysis, our data suggested that the combination of biological, physical, and chemical characteristics of forest soils created distinct conditions favoring the nitrogen biogeochemical cycle and that bacterial communities in undisturbed acidic forest soils were quite stable during seasonal change.

Antarctic DNA moving forward: genomic plasticity and biotechnological potential

Antarctica is the coldest, driest, and windiest continent, where only cold-adapted organisms survive. It has been frequently cited as a pristine place, but it has a highly diverse microbial community that is continually seeded by nonindigenous microorganisms. In addition to the intromission of 'alien' microorganisms, global warming strongly affects microbial Antarctic communities, changing the genes (qualitatively and quantitatively) potentially available for horizontal gene transfer. Several mobile genetic elements have been described in Antarctic bacteria (including plasmids, transposons, integrons, and genomic islands), and the data support that they are actively involved in bacterial evolution in the Antarctic environment. In addition, this environment is a genomic source for the identification of novel molecules, and many investigators have used culture-dependent and culture-independent approaches to identify cold-adapted proteins. Some of them are described in this review. We also describe studies for the design of new recombinant technologies for the production of 'difficult' proteins.