Heterotrophic denitrification at extremely high salt and pH by haloalkaliphilic Gammaproteobacteria from hypersaline soda lakes

Differences of bacterioplankton communities between the source and upstream regions of the Yangtze River: microbial structure, co-occurrence pattern, and environmental influencing factors

The source area of the Yangtze River is located in the hinterland of the Qinghai-Tibet Plateau, which is known as the "Earth's third pole." It is the water conservation area and the natural barrier of the ecosystem of the Yangtze River basin. It is also the most sensitive area of the natural ecosystem, and the ecological environment is very fragile. Microorganisms play key roles in the biogeochemical processes of water. In this paper, the bacterioplankton communities in the source and upstream regions of the Yangtze River were studied based on 16S rRNA high-throughput sequencing, and their environmental influencing factors were further analyzed. Results showed that the upstream region had higher richness and diversity than the source region. The predominant bacterial phyla in the source and upstream regions were Proteobacteria, Firmicutes, and Actinobacteriota. The bacterial phyla associated with municipal pollution and opportunistic pathogen, such as Firmicutes and Actinobacteriota, were more abundant in the upstream. By contrast, distinct planktonic bacterial genera associated with mining pollution, such as Acidiphilium and Acidithiobacillus, were more abundant in the source region. The co-occurrence network showed that the interaction of bacterioplankton community is more frequent in the upstream. The bacterioplankton community compositions, richness, and functional profiles were affected by the spatial heterogeneity. Moreover, variation partitioning analysis further confirmed that the amount of variation in the source region independently explained by variables of altitude was the largest, followed by water nutrient. This paper revealed the spatial distribution of planktonic bacterial communities in the source and upstream regions of the Yangtze River and its correlation with environmental factors, providing information support for ensuring the health and safety of aquatic ecosystems in the Yangtze River Basin.

Shifts in the bacterial community caused by combined pollutant loads in the North Canal River, China

A typical anthropogenically disturbed urban river polluted by a combination of conventional pollutants (nitrogen and phosphorus pollution) and heavy metals was investigated along a 238 km stretch. Changes in the bacterial community were evaluated using high-throughput sequencing, and the relationships between bacteria, heavy metals, and conventional pollutants were investigated. There was large spatial heterogeneity in the bacterial community along the river, and bacterial diversity in the upstream and midstream sections was much higher than in the downstream section. Heavy metals and conventional pollutants both exhibited close correlations with bacterial diversity and composition. For instance, potential fecal indicator bacteria, sewage indicator bacteria and pathogenic bacteria, such as Ruminococcus and Pseudomonas, were closely associated with Cu, Zn, and NH₄⁺-N. Rather than conventional pollutants, heavy metals were the main driving factors of the microbial community characteristics. These results confirm that bacterial communities play a crucial role in biogeochemical cycles. Therefore, heavy metals could be used as biomarkers of complex pollution to indicate the pollution status of riverine ecosystems and contribute to the restoration of habitats in anthropogenically disturbed urban rivers.

PMo12 as a redox mediator for bio-reduction of Cr(VI): Promotor or inhibitor?

Slow reduction rate and low reduction ability were the main limitations of bio-reduction of Cr(VI). As an efficient redox mediator, how phosphomolybdic acid (PMo₁₂) affected bio-reduction of Cr(VI) was worthy of exploration. In this study, short-term and long-term effects of PMo₁₂ on Cr(VI) reduction were investigated to reveal the relevant mechanism. After evaluating the short-term effect of PMo₁₂ concentration from 0.05 to 1.00 mM on Cr(VI) bio-reduction, 0.50 mM was found to be optimum by improving Cr(VI) reduction rate by 16.3 % and microbial electron transport system activity (ETSA) by 43.0 % with Cr(VI) reduction efficiency of 100 % in short-term (22 h) batch experiments. By contrast, in long-term (28 days) continuous flow experiments, 0.50 mM PMo₁₂ exhibited serious inhibition on Cr(VI) bio-reduction. The cumulative toxicity of Mo, strong oxidative stress (reactive oxygen species increased by 16.5 %), the inhibition of extracellular polymeric substances production and the reduction of microbial activity were proved to be the main inhibition mechanism. In terms of microbial electron transport system, the main electron carriers including flavin mononucleotide (FMN), nitrate reductase (NAR), nitrite reductase (NIR) were seriously inhibited. BugBase analysis confirmed that the relative abundance of biofilm forming bacteria decreased after PMo₁₂ addition, and the relative abundance of oxidative stress tolerance bacteria continued to increase.

Effects of Different Types of Human Disturbance on Total and Nitrogen-Transforming Bacteria in Haihe River

Haihe River is the largest water system in North China and is injected into the Bohai Sea in Tianjin City. In this study, different types of human disturbance (urban sewage, industrial pollution, ship disturbance) were selected from the upper reaches of Haihe river Tianjin section down to the estuary that connected with Bohai Sea for evaluation. By metagenomic sequencing, the effects of different types of disturbances on bacteria communities in Haihe sediments were studied, with a special focus on the function of nitrogen-cycling bacteria that were further analyzed through KEGG comparison. By analyzing the physical and chemical characteristics of sediments, results showed that human disturbance caused a large amount of nitrogen input into Haihe River, and different types of human disturbance led to distinct spatial heterogeneity in different sections of Haihe River. The bacteria community was dominated by Proteobacteria, followed by Chloroflexi, Bacteroidetes, Actinobacteria and Acidobacteria. The relative abundance of each phylum varied at different sites as a response to different types of human disturbances. In nitrogen cycling, microorganisms including nitrogen fixation and removal were detected at each site, which indicated the active potential for nitrogen transformation in Haihe River. In addition, a large number of metabolic pathways relating to human diseases were also revealed in urban and pollution sites by function potential, which provided an important basis for the indicative role of urban river ecosystem for public health security. In summary, by evaluating both the ecological role and function potential of bacteria in Haihe River under different types of human disturbance, the knowledge of microorganisms for healthy and disturbed river ecosystems has been broadened, which is also informative for further river management and bioremediation.

pH and microbial community determine the denitrifying activity in the presence of nitrate-containing radioactive waste

An important fraction of the currently stored volume of long-lived intermediate-level radioactive waste in Belgium contains large amounts of NaNO₃ homogeneously dispersed in a hard bituminous matrix. Geological disposal of this waste form in a water-saturated sedimentary formation such as Boom Clay will result in the leaching of high concentrations of NaNO₃, which could cause a geochemical perturbation of the surrounding clay, possibly affecting some of the favorable characteristics of the host formation. In addition, hyper-alkaline conditions are expected for thousands of years, imposed by the cementitious materials used as backfill material. Microbial nitrate reduction is a well-known process and can result in the accumulation of nitrite or nitrogenous gases. This could lead to the oxidation of redox-active Boom Clay components, which could (locally) decrease the reducing capacity of the clay formation. Here, we compared nitrate reduction processes between two microbial communities at different pH related to a geological repository environment and in the presence of a nitrate-containing waste simulate during 1 year in batch experiments. We showed that the microbial community from in Boom Clay borehole water was able to carry out nitrate reduction in the presence of acetate at pH 10.5, although the maximum rate of 1.3 ± 0.2 mM NO₃ ^-/day was much lower compared to that observed at pH 9 (2.9 mM NO₃ ^-/day). However, microbial activity at pH 10.5 was likely limited by a phosphate shortage. This study further confirmed that the Harpur Hill sediment harbors a microbial community adapted to high pH conditions. It reduced twice as much nitrate at pH 10.5 compared to pH 9 and the maximum nitrate reduction rate was higher at pH 10.5 compared to that at pH 9, i.e., 3.4 ± 0.8 mM NO₃ ^-/day versus 2.2 ± 0.4 mM NO₃ ^-/day. Both communities were able to form biofilms on non-radioactive Eurobitum. However, for both microbial communities, pH 12.5 seems to be a limiting condition for microbial activity as no nitrate reduction nor biofilm was observed. Nevertheless, pH alone is not sufficient to eliminate microbial presence, but it can induce a significant shift in the microbial community composition and reduce its nitrate reducing activity. Furthermore, at the interface between the cementitious disposal gallery and the clay host rock, the pH will not be sufficiently high to inhibit microbial nitrate reduction.

The role of coupled DNRA-Anammox during nitrate removal in a highly saline lake

Nitrate (NO₃^-) removal from aquatic ecosystems involves several microbially mediated processes, including denitrification, dissimilatory nitrate reduction to ammonium (DNRA), and anaerobic ammonium oxidation (anammox), controlled by slight changes in environmental gradients. In addition, some of these processes (i.e. denitrification) may involve the production of undesirable compounds such as nitrous oxide (N₂O), an important greenhouse gas. Saline lakes are prone to the accumulation of anthropogenic contaminants, making them highly vulnerable environments to NO₃^- pollution. The aim of this paper was to investigate the effect of light and oxygen on the different NO₃^- removal pathways under highly saline conditions. For this purpose, mesocosm experiments were performed using lacustrine, undisturbed, organic-rich sediments from the Pétrola Lake (Spain), a highly saline waterbody subject to anthropogenic NO₃^- pollution. The revised ¹⁵N-isotope pairing technique (¹⁵N-IPT) was used to determine NO₃^- sink processes. Our results demonstrate for the first time the coexistence of denitrification, DNRA, and anammox processes in a highly saline lake, and how their contribution was determined by environmental conditions (oxygen and light). DNRA, and especially denitrification to N₂O, were the dominant nitrogen (N) removal pathways when oxygen and/or light were present (up to 82%). In contrast, anoxia and darkness promoted NO₃^- reduction by DNRA (52%), combined with N loss by anammox (28%). Our results highlight the role of coupled DNRA-anammox, which has not yet been investigated in lacustrine sediments. We conclude that anoxia and darkness favored DNRA and anammox processes over denitrification and therefore to restrict N₂O emissions to the atmosphere.

Enhanced nitrogen removal from low-temperature wastewater by an iterative screening of cold-tolerant denitrifying bacteria

The biological process to remove nitrogen in winter effluent is often seriously compromised due to the effect of low temperatures (< 13 °C) on the metabolic activity of microorganisms. In this study, a novel heterotrophic nitrifying-aerobic denitrifying bacterium with cold tolerance was isolated by iterative domestication and named Moraxella sp. LT-01. The LT-01 maintained almost 60% of its maximal growth activity at 10 °C. Under initial concentrations of 100 mg/L, the removal efficiencies of ammonium, nitrate, nitrite by LT-01 were 70.3%, 65.4%, 61.7% respectively for 72 h incubation at 10 °C. Nitrogen balance analysis showed that about 46% of TN was released as gases and 16% of TN was assimilated for cell growth. The biomarker genes involved in nitrification and denitrification pathways were identified by gene-specific PCR and revealed that the LT-01 has nitrite reductase (NirS) but not hydroxylamine reductase (HAO), which implies the involvement of other genes in the process. The study indicates that LT-01 has the potential for use in low-temperature regions for efficient sewage treatment.

Metabarcoding under Brine: Microbial Ecology of Five Hypersaline Lakes at Rottnest Island (WA, Australia)

Hypersaline ecosystems—aquatic environments where concentration of salt exceeds 35 g L−1—host microbial communities that are highly specialised to cope with these extreme conditions. However, our knowledge on the taxonomic diversity and functional metabolisms characterising microbial communities in the water columns of hypersaline ecosystems is still limited, and this may compromise the future preservation of these unique environments. DNA metabarcoding provides a reliable and affordable tool to investigate environmental dynamics of aquatic ecosystems, and its use in brine can be highly informative. Here, we make use of bacterial 16S metabarcoding techniques combined with hydrochemical analyses to investigate the microbial patterns (diversity and functions) from five hypersaline lakes located at Rottnest Island (WA). Our results indicate lake-driven microbial aquatic assemblages that are characterised by taxonomically and functionally moderately to extremely halophilic groups, with TDS (total dissolved solids) and alkalinity amongst the most influential parameters driving the community patterns. Overall, our findings suggest that DNA metabarcoding allows rapid but reliable ecological assessment of the hypersaline aquatic microbial communities at Rottnest Island. Further studies involving different hypersaline lakes across multiple seasons will help elucidate the full extent of the potential of this tool in brine.

Response of the microbial community to salt stress and its stratified effect in constructed wetlands

Nitrogen removal in constructed wetlands (CWs) may be inhibited by salinity. The clarification of the response of microbial community to salt stress is a premise for developing strategies to improve nitrogen removal efficiency in CWs under saline conditions. Results showed that the ammonia nitrogen (NH₄⁺-N), nitrate nitrogen (NO₃^--N), and total nitrogen (TN) removal percentages significantly (p < 0.05) decreased in CWs with increasing salinity. The structure and abundance of the microbial community varied with different salinity levels and sampling depths in CWs. Compared with a non-saline condition, the abundances of some bacteria with a denitrification function (e.g., Arthrobacter) significantly (p < 0.05) decreased in CWs under saline conditions (i.e., EC of 15 and 30 mS/cm). Aerobic bacteria (e.g., Sphingomonas) exhibited more abundance in soil and upper gravel samples in CWs than those in bottom gravel samples, while the abundance of some denitrifying bacteria (e.g., Thauera and Azoarcus) was significantly (p < 0.05) higher in bottom gravel samples compared with soil and upper gravel samples, respectively. This study provides both microbiological evidence for explaining the impact of salt stress on nitrogen removal in CWs and scientific reference for developing enhanced strategies to improve the nitrogen removal capacity of CWs.

Spatial distribution and influencing factors on the variation of bacterial communities in an urban river sediment

The water and sediments of urban rivers are spatially heterogeneous because of the influence of environmental and anthropogenic factors. However, the spatial and functional diversity of bacterial communities in urban river sediments are unclear. We investigated the spatial distribution of microbial compositions in sediments in Qingdao section of the Dagu River, and the effects of sediment physiochemical properties on the variation were explored. Among the seven heavy metals analyzed, only the average concentration of Cd significantly exceeded the safety limit for sediments. The detailed composition and spatial distribution of bacterial communities fluctuated substantially between sites along the river. Bacterial datasets were separated into three clusters according to the environmental characteristics of sampling areas (the urbanized, scenic, and intertidal zones). For the urbanized zone, Acidobacteria, Firmicutes, Gemmatimonadetes, Bacteroidetes, and Gammaproteobacteria were significantly enriched, implying the effects of human activity. In the intertidal zone, Alphaproteobacteria and Deltaproteobacteria were significantly enriched, which are associated with S redox processes, as in the marine environment. Variation partitioning analysis showed that the amount of variation independently explained by variables of Na, Al, total S and Zn was largest, followed by sediment nutrients, while heavy metals and pH explained independently 13% and 9% of the variance, respectively. Overall, microbial structures in the Dagu River exhibited spatial variation and functional diversity as a result of natural and anthropogenic factors. The results will enable the prediction of the changes in urban river ecosystems that maintain their ecological balance and health.

Nitrate and nitrite bacterial reduction at alkaline pH and high nitrate concentrations, comparison of acetate versus dihydrogen as electron donors

This study assesses bacterial denitrification at alkaline pH, up to 12, and high nitrate concentration, up to 400 mM. Two types of electron donors organic (acetate) and inorganic (dihydrogen) were compared. With both types of electron donors, nitrite reduction was the key step, likely to increase the pH and lead to nitrite accumulation. Firstly, an acclimation process was used: nitrate was progressively increased in three cultures set at pH 9, 10, or 11. This method allowed to observe for the first time nitrate reduction up to pH 10 and 100 mM nitrate with dihydrogen, or up to pH 10 and 400 mM nitrate with acetate. Nitrate reduction kinetics were faster in the presence of acetate. To investigate further the impact of the type of electron donor, a transition from acetate to dihydrogen was tested, and the pH evolution was modelled. Denitrification with dihydrogen strongly increases the pH while with acetate the pH evolution depends on the initial pH. The main difference is the production of acidifying CO₂ during the acetate oxidation. Finally, the use of long duration cultures with a highly alkaline pH allowed a nitrate reduction up to pH 11.5 with acetate. However, no reduction was possible in hydrogenotrophy as it would have increased the pH further. Instead, bacteria used organic matter from inoculum to reduce nitrate at pH 11.5. Therefore, considering bacterial denitrification in a context of alkaline pH and high nitrate concentration an organic electron donor such as acetate is advantageous.

Influence of Hydrogen Electron Donor, Alkaline pH, and High Nitrate Concentrations on Microbial Denitrification: A Review

Bacterial respiration of nitrate is a natural process of nitrate reduction, which has been industrialized to treat anthropic nitrate pollution. This process, also known as “microbial denitrification”, is widely documented from the fundamental and engineering points of view for the enhancement of the removal of nitrate in wastewater. For this purpose, experiments are generally conducted with heterotrophic microbial metabolism, neutral pH and moderate nitrate concentrations (<50 mM). The present review focuses on a different approach as it aims to understand the effects of hydrogenotrophy, alkaline pH and high nitrate concentration on microbial denitrification. Hydrogen has a high energy content but its low solubility, 0.74 mM (1 atm, 30 °C), in aqueous medium limits its bioavailability, putting it at a kinetic disadvantage compared to more soluble organic compounds. For most bacteria, the optimal pH varies between 7.5 and 9.5. Outside this range, denitrification is slowed down and nitrite (NO₂⁻) accumulates. Some alkaliphilic bacteria are able to express denitrifying activity at pH levels close to 12 thanks to specific adaptation and resistance mechanisms detailed in this manuscript, and some bacterial populations support nitrate concentrations in the range of several hundred mM to 1 M. A high concentration of nitrate generally leads to an accumulation of nitrite. Nitrite accumulation can inhibit bacterial activity and may be a cause of cell death.

A shared core microbiome in soda lakes separated by large distances

In alkaline soda lakes, concentrated dissolved carbonates establish productive phototrophic microbial mats. Here we show how microbial phototrophs and autotrophs contribute to this exceptional productivity. Amplicon and shotgun DNA sequencing data of microbial mats from four Canadian soda lakes indicate the presence of > 2,000 species of Bacteria and Eukaryotes. We recover metagenome-assembled-genomes for a core microbiome of < 100 abundant bacteria, present in all four lakes. Most of these are related to microbes previously detected in sediments of Asian alkaline lakes, showing that common selection principles drive community assembly from a globally distributed reservoir of alkaliphile biodiversity. Detection of > 7,000 proteins show how phototrophic populations allocate resources to specific processes and occupy complementary niches. Carbon fixation proceeds by the Calvin-Benson-Bassham cycle, in Cyanobacteria, Gammaproteobacteria, and, surprisingly, Gemmatimonadetes. Our study provides insight into soda lake ecology, as well as a template to guide efforts to engineer biotechnology for carbon dioxide conversion.

Efecto del compost en la diversidad de bacterias rizosféricas del cultivo de morera (Morus alba)

La producción orgánica de seda incluye la aplicación de compost como practica de cultivo en morera (Morus alba), sin embargo, el efecto de la fertilización orgánica en las poblaciones de bacterias rizosféricas no siempre es positivo. Para evaluar el efecto del compost en la diversidad de bacterias rizosféricas en cultivos de morera (Morus alba), se aplicaron 0, 0.25, 0.5 y 1 kg.m-2 de compost a parcelas con morera dispuestas en un diseño en bloques completos al azar. De cada parcela se extrajo ADN del suelo rizosférico a los 0, 5, 10 y 90 días de aplicado el compost y se amplificó la región V4 del gen ADNr 16S para su secuenciación y asignación taxonómica de los OTUS. Los índices de diversidad alpha mostraron la dominancia de algunos grupos taxonómicos, como los phyla Proteobacteria y Acidobacteria y los géneros Pseudomonas, Opitutus, Luteolibacter y Nitrospir. La diversidad beta indicó similitud entre las muestras influenciadas por la aplicación compost y el incremento de la diversidad en las parcelas muestreadas al final del experimento (90 días). Los grupos taxonómicos dominantes se caracterizan por su función en el ciclo del nitrógeno. Así, se concluyó que la aplicación de 1 kg.m-2 llevó al aumento de la humedad del suelo, el pH y la disponibilidad de nutrientes, lo que incremento la diversidad de bacterias rizosféricas con cambios positivos en composición, riqueza y abundancia en los niveles de orden, familia y género.

Diversity, structure, and size of N(2)O-producing microbial communities in soils--what matters for their functioning?

Nitrous oxide (N(2)O) is mainly generated via nitrification and denitrification processes in soils and subsequently emitted into the atmosphere where it causes well-known radiative effects. How nitrification and denitrification are affected by proximal and distal controls has been studied extensively in the past. The importance of the underlying microbial communities, however, has been acknowledged only recently. Particularly, the application of molecular methods to study nitrifiers and denitrifiers directly in their habitats enabled addressing how environmental factors influence the diversity, community composition, and size of these functional groups in soils and whether this is of relevance for their functioning and N(2)O production. In this review, we summarize the current knowledge on community-function interrelationships. Aerobic nitrification (ammonia oxidation) and anaerobic denitrification are clearly under different controls. While N(2)O is an obligatory intermediate in denitrification, its production during ammonia oxidation depends on whether nitrite, the end product, is further reduced. Moreover, individual strains vary strongly in their responses to environmental cues, and so does N(2)O production. We therefore conclude that size and structure of both functional groups are relevant with regard to production and emission of N(2)O from soils. Diversity affects on function, however, are much more difficult to assess, as it is not resolved as yet how individual nitrification or denitrification genotypes are related to N(2)O production. More research is needed for further insights into the relation of microbial communities to ecosystem functions, for instance, how the actively nitrifying or denitrifying part of the community may be related to N(2)O emission.

Anaerobic Metabolism in Haloferax Genus: Denitrification as Case of Study

A number of species of Haloferax genus (halophilic archaea) are able to grow microaerobically or even anaerobically using different alternative electron acceptors such as fumarate, nitrate, chlorate, dimethyl sulphoxide, sulphide and/or trimethylamine. This metabolic capability is also shown by other species of the Halobacteriaceae and Haloferacaceae families (Archaea domain) and it has been mainly tested by physiological studies where cell growth is observed under anaerobic conditions in the presence of the mentioned compounds. This work summarises the main reported features on anaerobic metabolism in the Haloferax, one of the better described haloarchaeal genus with significant potential uses in biotechnology and bioremediation. Special attention has been paid to denitrification, also called nitrate respiration. This pathway has been studied so far from Haloferax mediterranei and Haloferax denitrificans mainly from biochemical point of view (purification and characterisation of the enzymes catalysing the two first reactions). However, gene expression and gene regulation is far from known at the time of writing this chapter.

Treatment of Alkaline Cr(VI)-Contaminated Leachate with an Alkaliphilic Metal-Reducing Bacterium

Chromium in its toxic Cr(VI) valence state is a common contaminant particularly associated with alkaline environments. A well-publicized case of this occurred in Glasgow, United Kingdom, where poorly controlled disposal of a cementitious industrial by-product, chromite ore processing residue (COPR), has resulted in extensive contamination by Cr(VI)-contaminated alkaline leachates. In the search for viable bioremediation treatments for Cr(VI), a variety of bacteria that are capable of reduction of the toxic and highly soluble Cr(VI) to the relatively nontoxic and less mobile Cr(III) oxidation state, predominantly under circumneutral pH conditions, have been isolated. Recently, however, alkaliphilic bacteria that have the potential to reduce Cr(VI) under alkaline conditions have been identified. This study focuses on the application of a metal-reducing bacterium to the remediation of alkaline Cr(VI)-contaminated leachates from COPR. This bacterium, belonging to the Halomonas genus, was found to exhibit growth concomitant to Cr(VI) reduction under alkaline conditions (pH 10). Bacterial cells were able to rapidly remove high concentrations of aqueous Cr(VI) (2.5 mM) under anaerobic conditions, up to a starting pH of 11. Cr(VI) reduction rates were controlled by pH, with slower removal observed at pH 11, compared to pH 10, while no removal was observed at pH 12. The reduction of aqueous Cr(VI) resulted in the precipitation of Cr(III) biominerals, which were characterized using transmission electron microscopy and energy-dispersive X-ray analysis (TEM-EDX) and X-ray photoelectron spectroscopy (XPS). The effectiveness of this haloalkaliphilic bacterium for Cr(VI) reduction at high pH suggests potential for its use as an in situ treatment of COPR and other alkaline Cr(VI)-contaminated environments.

Functional microbiology of soda lakes

Soda lakes represent unique permanently haloalkaline system. Despite the harsh conditions, they are inhabited by abundant, mostly prokaryotic, microbial communities. This review summarizes results of studies of main functional groups of the soda lake prokaryotes responsible for carbon, nitrogen and sulfur cycling, including oxygenic and anoxygenic phototrophs, aerobic chemolithotrophs, fermenting and respiring anaerobes. The main conclusion from this work is that the soda lakes are very different from other high-salt systems in respect to microbial richness and activity. The reason for this difference is determined by the major physico-chemical features of two dominant salts - NaCl in neutral saline systems and sodium carbonates in soda lakes, that are influencing the amount of energy required for osmotic adaptation.

Effect of temperature, salinity, heavy metals, ammonium concentration, pH and dissolved oxygen on ammonium removal by an aerobic nitrifier

An aerobic nitrifier WY-01 was identified asAlcaligenes faecalisby its 16S rRNA gene sequence analysis. It could remove ammonium effectively in varying physico-chemical conditions, such as low temperature, high salinity and high ammonium loads.

How could haloalkaliphilic microorganisms contribute to biotechnology?

Haloalkaliphiles are microorganisms requiring Na+concentrations of at least 0.5 mol·L–1and an alkaline pH of 9 for optimal growth. Their unique features enable them to make significant contributions to a wide array of biotechnological applications. Organic compatible solutes produced by haloalkaliphiles, such as ectoine and glycine betaine, are correlated with osmoadaptation and may serve as stabilizers of intracellular proteins, salt antagonists, osmoprotectants, and dermatological moisturizers. Haloalkaliphiles are an important source of secondary metabolites like rhodopsin, polyhydroxyalkanoates, and exopolysaccharides that play essential roles in biogeocycling organic compounds. These microorganisms also can secrete unique exoenzymes, including proteases, amylases, and cellulases, that are highly active and stable in extreme haloalkaline conditions and can be used for the production of laundry detergent. Furthermore, the unique metabolic pathways of haloalkaliphiles can be applied in the biodegradation and (or) biotransformation of a broad range of toxic industrial pollutants and heavy metals, in wastewater treatment, and in the biofuel industry.

Diversity and distribution of Halomonas in Rambla Salada, a hypersaline environment in the southeast of Spain

We have studied the diversity and distribution of Halomonas populations in the hypersaline habitat Rambla Salada (Murcia, southeastern Spain) by using different molecular techniques. Denaturing gradient gel electrophoresis (DGGE) using specific primers for the 16S rRNA gene of Halomonas followed by a multivariate analysis of the results indicated that richness and evenness of the Halomonas populations were mainly influenced by the season. We found no significant differences between the types of samples studied, from either watery sediments or soil samples. The highest value of diversity was reached in June 2006, the season with the highest salinity. Furthermore, canonical correspondence analysis (CCA) demonstrated that both salinity and pH significantly affected the structure of the Halomonas community. Halomonas almeriensis and two denitrifiers, H. ilicicola and H. ventosae were the predominant species. CARD-FISH showed that the percentage of Halomonas cells with respect to the total number of microorganisms ranged from 4.4% to 5.7%. To study the functional role of denitrifying species, we designed new primer sets targeting denitrification nirS and nosZ genes. Using these primers, we analyzed sediments from the upwelling zone collected in June 2006, where we found the highest percentage of denitrifiers (74%). Halomonas ventosae was the predominant denitrifier in this site.

Marinobacter hydrocarbonoclasticus NY-4, a novel denitrifying, moderately halophilic marine bacterium

The isolation and characterization of a novel halophilic denitrifying marine bacterium is described. The halophilic bacterium, designated as NY-4, was isolated from soil in Yancheng City, China, and identified as Marinobacter hydrocarbonoclasticus by 16S rRNA gene sequence phylogenetic analysis. This organism can grow in NaCl concentrations ranging from 20 to 120 g/L. Optimum growth occurs at 80 g/L NaCl and pH 8.0. The organism can grow on a broad range of carbon sources and demonstrated efficient denitrifying ability (94.2% of nitrate removal and 80.9% of total nitrogen removal in 48 h). During denitrification by NY-4, no NO₂^--N was accumulated, N₂ was the only gaseous product and no harmful N₂O was produced. Because of its rapid denitrification ability, broad carbon use range and ability to grow under high salinity and pH conditions, NY-4 holds promise for the treatment of saline waste waters.

Genetic characterization of denitrifier communities with contrasting intrinsic functional traits

Microorganisms capable of denitrification are polyphyletic and exhibit distinct denitrification regulatory phenotypes (DRP), and thus, denitrification in soils could be controlled by community composition. In a companion study (Dörsch et al., 2012) and preceding work, ex situ denitrification assays of three organic soils demonstrated profoundly different functional traits including N(2) O/N(2) ratios. Here, we explored the composition of the underlying denitrifier communities by analyzing the abundance and structure of denitrification genes (nirK, nirS, and nosZ). The relative abundance of nosZ (vs. nirK + nirS) was similar for all communities, and hence, the low N(2) O reductase activity in one of the soils was not because of the lack of organisms with this gene. Similarity in community composition between the soils was generally low for nirK and nirS, but not for nosZ. The community with the most robust denitrification (consistently low N(2) O/N(2) ) had the highest diversity/richness of nosZ and nirK, but not of nirS. Contrary results found for a second soil agreed with impaired denitrification (low overall denitrification activity, high N(2) O/N(2) ). In conclusion, differences in community composition and in the absolute abundance of denitrification genes clearly reflected the functional differences observed in laboratory studies and may shed light on differences in in situ N(2) O emission of the soils.

Gammaproteobacteria occurrence and microdiversity in Tyrrhenian Sea sediments as revealed by cultivation-dependent and -independent approaches

Bacterial diversity in Tyrrhenian Sea sediments was assessed using cultivation-dependent and -independent approaches. Samples collected from the different sediment layers (up to 30cm) relative to four seamount and non-seamount stations, at depths from 3425 to 3580m, were subjected to DNA extraction and 16S rRNA amplification targeting the V3 region. Denaturing gradient gel electrophoresis (DGGE) showed several heterogeneous profiles and 27 single bands were excised and sequenced. Sequence analysis revealed the presence of Firmicutes, Actinobacteria and Chloroflexi in 26% of the DGGE bands and a predominance of sequences affiliated to cultivable and uncultivable clones of Gammaproteobacteria (55%). To corroborate these findings, cultivation attempts were performed that allowed the isolation of 87 strains assigned to the proteobacterial classes. Identification was achieved by means of automated ribosomal intergenic spacer analysis (ARISA) and by 16S rDNA sequencing. The isolates were related to the gamma, alpha and beta subclasses of Proteobacteria with respective percentages of 77, 17 and 6%. The most predominant Gammaproteobacteria isolates, assigned to the Psychrobacter marincola and P. submarinus clade (n=53) and to Halomonas aquamarina (n=14), showed a huge intraspecific diversity with 29 distinct ARISA haplotypes. The detection by both approaches of these psychrophilic and moderately halophilic species and their extensive microdiversity indicated their predominance in Tyrrhenian Sea sediments where they constituted the indigenous microflora.