Functional differentiation of nitrate-reducing isolates regulated by long-term fertilization in a rice paddy soil

Fertilization can cause obvious shifts in nitrate-reducing community composition in agricultural ecosystems; however, little is known about the behaviors and functional characters of isolated nitrate reducers adapted to a specific environment. In this study, 849 nitrate-reducing bacteria were isolated from various fertilization treatments in a long-term paddy field experiment; the isolates were further characterized in functions with both culture-dependent and independent methodologies. The results showed that CK (no fertilizer) treatment had four genera with even relative abundance, whereas the other three treatments had their own predominant genera with Chromobacterium in nitrogen (N) fertilizer, Serratia in NPK (nitrogen, phosphorus, and potassium fertilizer) and Enterobacter in NPKC treatment (NPK plus rice straw). The isolates of Serratia and Enterobacter grew faster and produced significantly more nitrites than those of Chromobacterium and Burkholderia in the normal growth medium, suggesting that the dominant isolates from nutrient-rich environment, such as NPK and NPKC treatments, are better adapted to high nutritional conditions. On the contrary, the strains of Chromobacterium and Burkholderia possessed stronger nitrite production ability in comparison with the isolates of Serratia and Enterobacter in the diluted growth medium, indicating that the selected isolates from CK and N treatments have the capability to develop under nutrient-limiting conditions. Our results indicated that the behaviors and functions of nitrate reducers appears to be important in adapting to their dwelling habitats.

Microbial diversity of the Arabian Sea in the Oxygen minimum zones by metagenomics approach

ABSTRACTLarge oxygen depleted areas known as oxygen minimum zones (OMZ) have been observed in the Arabian Sea and recent reports indicate that these areas are expanding at an alarming rate. In marine waters, oxygen depletion may also be related to global warming and the temperature rise, acidification and deoxygenation can lead to major consequences wherein the plants, fish and other biota will struggle to survive in the ecosystem.The current study has identified the microbial community structure using NGS based metagenomics analysis in the water samples collected at different depth from the oxygen depleted and non-OMZ areas of Arabian Sea. Environmental variables such as depth, site of collection and oxygen concentration appeared to influence the species richness and evenness among microbial communities in these locations. Our observations clearly indicate that population dynamics of microbes consisting of nitrate reducers accompanied by sulphate reducers and sulphur oxidizers participate in the interconnected geochemical cycles of the OMZ areas. In addition to providing baseline data related to the diversity and microbial community dynamics in oxygen-depleted water in the OMZ; such analysis can provide insight into processes regulating productivity and ecological community structure of the ocean.

Taxonomic and Functional Annotation of Termite Degraded Butea monosperma (Lam.) Kuntze (Flame of the Forest)

Background: Butea monosperma is an economically and medicinally important plant that grows all over India, however, the plant is highly susceptible to termite attack. The present study unravelled the bacterial community composition and their functional attributions from the termite degraded Butea. Methods: Total genomic DNA from termite degraded Butea monosperma samples was extracted and subjected to sequencing on Illumina's Miseq. The raw and unassembled reads obtained from high-throughput sequencing were used for taxonomic and functional profiling using different online and stand-alone softwares. Moreover, to ascertain the effect of different geographical locations and environmental factors, comparative analysis was performed using four other publically available metagenomes. Results: The higher abundance of Actinobacteria (21.27%), Proteobacteria (14.18%), Firmicutes (10.46%), and Bacteroidetes (4.11%) was found at the phylum level. The genus level was dominated by Bacillus (4.33%), Gemmatimonas (3.13%), Mycobacterium (1.82%), Acidimicrobium (1.69%), Thermoleophilum (1.23%), Nocardioides (1.44%), Terrimonas and Acidithermus (1.09%) and Clostridium (1.05%). Functional annotation of the termite degraded B. monosperma metagenome revealed a high abundance of ammonia oxidizers, sulfate reducers, dehalogenators, nitrate reducers, sulfide oxidizers, xylan degraders, nitrogen fixers and chitin degraders. Conclusion: The present study highlights the significance of the inherent microbiome of the degraded Butea shaping the microbial communities for effective degradation of biomass and different environmental toxicants. The unknown bacterial communities present in the sample can serve as enzyme sources for lignocelluloses degradation for biofuel production.

The changes in soil-biological processes and structure of microbial community of agrochernozems in conditions of different ways of soil cultivation

The impact of soil cultivation methods (tillage with soil overturning at a depth of 20-22 and 14-16 cm, beardless plowing and surface treatment respectively at a depth of 14-16 and 6-8 cm, and also zero or minimal tillage)) on biological activity of various ecology-trophic groups of microorganisms on agronochernozems of the Kamennaya Steppe (Voronezh oblast) using classical inoculation methods on elective media. It is shown that chernozems are highly resistant soils that are resistant to external impacts, preserving high biological activity even at the maximum mechanical treatment. Tillage with soil overturn leads to aeration of the arable horizon and the activity initiation of aerobic microorganisms of the carbon cycle, responsible for the mineralization of both complex and simple organic compounds of the soil. The contribution of microorganisms of the nitrogen cycle (nitrate-reducers and nitrogen fixers) to the overall biological activity of migratory-micellar chernozems of arable land and layland was minimal. The level of mechanical impact on the soil affects the quantitative indices and biological activity of microorganisms in the soil - the stronger the effect, the deeper layers are affected. The processes of entrance for fresh organic matter prevail over the processes of mineralization practically in all variants of the experiment, except for tillage with the soil overturn to a depth of 14-16 cm, as indicated by the values of the mineralization coefficients. The strongest humus-accumulative effect was observed in the variant with zero treatment, which is maximally approximated to such processes, occurred in a layland. Minimal soil cultivation will help to preserve the unique structure of chernozem soil, to increase the flow of fresh organic remains, to preserve the high biological diversity which is specific for natural biocenosises.

Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate-reducing benthic microbial populations

For the anaerobic remineralization of organic matter in marine sediments, sulfate reduction coupled to fermentation plays a key role. Here, we enriched sulfate-reducing/fermentative communities from intertidal sediments under defined conditions in continuous culture. We transiently exposed the cultures to oxygen or nitrate twice daily and investigated the community response. Chemical measurements, provisional genomes and transcriptomic profiles revealed trophic networks of microbial populations. Sulfate reducers coexisted with facultative nitrate reducers or aerobes enabling the community to adjust to nitrate or oxygen pulses. Exposure to oxygen and nitrate impacted the community structure, but did not suppress fermentation or sulfate reduction as community functions, highlighting their stability under dynamic conditions. The most abundant sulfate reducer in all cultures, related to Desulfotignum balticum , appeared to have coupled acetate oxidation to sulfate reduction. We described a novel representative of the widespread uncultured phylum Candidatus Fermentibacteria (formerly candidate division Hyd24-12). For this strictly anaerobic, obligate fermentative bacterium, we propose the name Ca. “Sabulitectum silens” and identify it as a partner of sulfate reducers in marine sediments. Overall, we provide insights into the metabolic network of fermentative and sulfate-reducing microbial populations, their niches, and adaptations to a dynamic environment.

Insights into Nitrate-Reducing Fe(II) Oxidation Mechanisms through Analysis of Cell-Mineral Associations, Cell Encrustation, and Mineralogy in the Chemolithoautotrophic Enrichment Culture KS

ABSTRACT Most described nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOB) are mixotrophic and depend on organic cosubstrates for growth. Encrustation of cells in Fe(III) minerals has been observed for mixotrophic NRFeOB but not for autotrophic phototrophic and microaerophilic Fe(II) oxidizers. So far, little is known about cell-mineral associations in the few existing autotrophic NRFeOB. Here, we investigate whether the designated autotrophic Fe(II)-oxidizing strain (closely related to Gallionella and Sideroxydans) or the heterotrophic nitrate reducers that are present in the autotrophic nitrate-reducing Fe(II)-oxidizing enrichment culture KS form mineral crusts during Fe(II) oxidation under autotrophic and mixotrophic conditions. In the mixed culture, we found no significant encrustation of any of the cells both during autotrophic oxidation of 8 to 10 mM Fe(II) coupled to nitrate reduction and during cultivation under mixotrophic conditions with 8 to 10 mM Fe(II), 5 mM acetate, and 4 mM nitrate, where higher numbers of heterotrophic nitrate reducers were present. Two pure cultures of heterotrophic nitrate reducers (Nocardioides and Rhodanobacter) isolated from culture KS were analyzed under mixotrophic growth conditions. We found green rust formation, no cell encrustation, and only a few mineral particles on some cell surfaces with 5 mM Fe(II) and some encrustation with 10 mM Fe(II). Our findings suggest that enzymatic, autotrophic Fe(II) oxidation coupled to nitrate reduction forms poorly crystalline Fe(III) oxyhydroxides and proceeds without cellular encrustation while indirect Fe(II) oxidation via heterotrophic nitrate-reduction-derived nitrite can lead to green rust as an intermediate mineral and significant cell encrustation. The extent of encrustation caused by indirect Fe(II) oxidation by reactive nitrogen species depends on Fe(II) concentrations and is probably negligible under environmental conditions in most habitats. IMPORTANCE Most described nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOB) are mixotrophic (their growth depends on organic cosubstrates) and can become encrusted in Fe(III) minerals. Encrustation is expected to be harmful and poses a threat to cells if it also occurs under environmentally relevant conditions. Nitrite produced during heterotrophic denitrification reacts with Fe(II) abiotically and is probably the reason for encrustation in mixotrophic NRFeOB. Little is known about cell-mineral associations in autotrophic NRFeOB such as the enrichment culture KS. Here, we show that no encrustation occurs in culture KS under autotrophic and mixotrophic conditions while heterotrophic nitrate-reducing isolates from culture KS become encrusted. These findings support the hypothesis that encrustation in mixotrophic cultures is caused by the abiotic reaction of Fe(II) with nitrite and provide evidence that Fe(II) oxidation in culture KS is enzymatic. Furthermore, we show that the extent of encrustation caused by indirect Fe(II) oxidation by reactive nitrogen species depends on Fe(II) concentrations and is probably negligible in most environmental habitats.

Potential Role of Nitrite for Abiotic Fe(II) Oxidation and Cell Encrustation during Nitrate Reduction by Denitrifying Bacteria

ABSTRACTMicroorganisms have been observed to oxidize Fe(II) at neutral pH under anoxic and microoxic conditions. While most of the mixotrophic nitrate-reducing Fe(II)-oxidizing bacteria become encrusted with Fe(III)-rich minerals, photoautotrophic and microaerophilic Fe(II) oxidizers avoid cell encrustation. The Fe(II) oxidation mechanisms and the reasons for encrustation remain largely unresolved. Here we used cultivation-based methods and electron microscopy to compare two previously described nitrate-reducing Fe(II) oxidizers (Acidovoraxsp. strain BoFeN1 andPseudogulbenkianiasp. strain 2002) and two heterotrophic nitrate reducers (Paracoccus denitrificansATCC 19367 andP. denitrificansPd 1222). All four strains oxidized ∼8 mM Fe(II) within 5 days in the presence of 5 mM acetate and accumulated nitrite (maximum concentrations of 0.8 to 1.0 mM) in the culture media. Iron(III) minerals, mainly goethite, formed and precipitated extracellularly in close proximity to the cell surface. Interestingly, mineral formation was also observed within the periplasm and cytoplasm; intracellular mineralization is expected to be physiologically disadvantageous, yet acetate consumption continued to be observed even at an advanced stage of Fe(II) oxidation. Extracellular polymeric substances (EPS) were detected by lectin staining with fluorescence microscopy, particularly in the presence of Fe(II), suggesting that EPS production is a response to Fe(II) toxicity or a strategy to decrease encrustation. Based on the data presented here, we propose a nitrite-driven, indirect mechanism of cell encrustation whereby nitrite forms during heterotrophic denitrification and abiotically oxidizes Fe(II). This work adds to the known assemblage of Fe(II)-oxidizing bacteria in nature and complicates our ability to delineate microbial Fe(II) oxidation in ancient microbes preserved as fossils in the geological record.

Actinobacterial Nitrate Reducers and Proteobacterial Denitrifiers Are Abundant in N2O-Metabolizing Palsa Peat

ABSTRACTPalsa peats are characterized by elevated, circular frost heaves (peat soil on top of a permanently frozen ice lens) and are strong to moderate sources or even temporary sinks for the greenhouse gas nitrous oxide (N2O). Palsa peats are predicted to react sensitively to global warming. The acidic palsa peat Skalluvaara (approximate pH 4.4) is located in the discontinuous permafrost zone in northwestern Finnish Lapland.In situN2O fluxes were spatially variable, ranging from 0.01 to −0.02 μmol of N2O m−2h−1. Fertilization with nitrate stimulatedin situN2O emissions and N2O production in anoxic microcosms without apparent delay. N2O was subsequently consumed in microcosms. Maximal reaction velocities (vmax) of nitrate-dependent denitrification approximated 3 and 1 nmol of N2O per h per gram (dry weight [gDW]) in soil from 0 to 20 cm and below 20 cm of depth, respectively.vmaxvalues of nitrite-dependent denitrification were 2- to 5-fold higher than thevmaxnitrate-dependent denitrification, andvmaxof N2O consumption was 1- to 6-fold higher than that of nitrite-dependent denitrification, highlighting a high N2O consumption potential. Up to 12 species-level operational taxonomic units (OTUs) ofnarG,nirKandnirS, andnosZwere retrieved. Detected OTUs suggested the presence of diverse uncultured soil denitrifiers and dissimilatory nitrate reducers, hitherto undetected species, as well asActino-,Alpha-, andBetaproteobacteria. Copy numbers ofnirSalways outnumbered those ofnirKby 2 orders of magnitude. Copy numbers ofnirStended to be higher, while copy numbers ofnarGandnosZtended to be lower in 0- to 20-cm soil than in soil below 20 cm. The collective data suggest that (i) the source and sink functions of palsa peat soils for N2O are associated with denitrification, (ii) actinobacterial nitrate reducers andnirS-type andnosZ-harboring proteobacterial denitrifiers are important players, and (iii) acidic soils like palsa peats represent reservoirs of diverse acid-tolerant denitrifiers associated with N2O fluxes.

Diversity, Abundance, and Potential Activity of Nitrifying and Nitrate-Reducing Microbial Assemblages in a Subglacial Ecosystem

ABSTRACTSubglacial sediments sampled from beneath Robertson Glacier (RG), Alberta, Canada, were shown to harbor diverse assemblages of potential nitrifiers, nitrate reducers, and diazotrophs, as assessed byamoA,narG, andnifHgene biomarker diversity. Although archaealamoAgenes were detected, they were less abundant and less diverse than bacterialamoA, suggesting that bacteria are the predominant nitrifiers in RG sediments. Maximum nitrification and nitrate reduction rates in microcosms incubated at 4°C were 280 and 18.5 nmol of N per g of dry weight sediment per day, respectively, indicating the potential for these processes to occurin situ. Geochemical analyses of subglacial sediment pore waters and bulk subglacial meltwaters revealed low concentrations of inorganic and organic nitrogen compounds. These data, when coupled with a C/N atomic ratio of dissolved organic matter in subglacial pore waters of ∼210, indicate that the sediment communities are N limited. This may reflect the combined biological activities of organic N mineralization, nitrification, and nitrate reduction. Despite evidence of N limitation and the detection ofnifH, we were unable to detect biological nitrogen fixation activity in subglacial sediments. Collectively, the results presented here suggest a role for nitrification and nitrate reduction in sustaining microbial life in subglacial environments. Considering that ice currently covers 11% of the terrestrial landmass and has covered significantly greater portions of Earth at times in the past, the demonstration of nitrification and nitrate reduction in subglacial environments furthers our understanding of the potential for these environments to contribute to global biogeochemical cycles on glacial-interglacial timescales.