Community diversity and abundance of ammonia-oxidizing archaea and bacteria in shrimp pond sediment at different culture stages.

AIMS: Ammonia oxidation is a significant process of nitrogen cycles in a lot of ecosystems sediments while there are few studies in shrimp culture pond (SCP) sediments. This paper attempted to explore the community diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in SCP sediments at different culture stages. METHODS AND RESULTS: We collected SCP sediments and analysed the community diversity and abundance of AOA and bacteria in shrimp pond sediment at different culture stages using the ammonia monooxygenase (amoA) gene with quantitative PCR (qPCR) and 16S rRNA gene sequencing. The AOB-amoA gene abundance was showed higher than AOA-amoA gene abundance in SCP sediments on Day 50 and Day 60 after shrimp larvae introducing into the pond, and the diversity of AOA in SCP sediments was higher than that of AOB. The phylogenetic tree revealed that the most of AOA were the member of Nitrosopumilus and Nitrososphaera, and the majority of AOB sequences were clustered into Nitrosospira, Nitrosomonas clusters 6a and 7. The AOA community has close relationship with total organic carbon (TOC), pH, total phosphorus (TP), nitrate reductase, urease, acid phosphatase and ß-glucosidase. The AOB community was related to TOC, C/N and nitrate reductase. CONCLUSIONS: AOA and AOB play the different ecological roles in SCP sediments at different culture stages. SIGNIFICANCE AND IMPACT OF THE STUDY: Our results suggested that the different community diversity and abundance of AOA and AOB in SCP sediments, which may improve our ecological cognition of shrimp culture stages in SCP ecosystems.

Comparison of chemical and microbiological changes during the aerobic composting and vermicomposting of green waste.

This research was conducted to compare chemical and microbiological properties during aerobic composting (AC) and vermicomposting (VC) of green waste. Relative to AC, VC significantly decreased the pH and lignin and cellulose contents, and significantly increased the electrical conductivity and total N and available P contents. For AC, BIrii41_norank (order Myxococcales) was the major bacterial genus at 30 d and again became dominant genus from 90-150 d, with relative abundances of 2.88% and 4.77-5.19%, respectively; at 45 d and 60 d, the dominant bacterial genus was Nitrosomonadaceae_uncultured (order Nitrosomonadales) with relative abundances of 2.83-7.17%. For VC, the dominant bacterial genus was BIrii41_norank (except at 45 d), which accounted for 2.11-7.96% of the total reads. The dominant fungal class was Sordariomycetes in AC (relative abundances 39.2-80.6%) and VC (relative abundances 42.1-69.5%). The abundances of microbial taxa and therefore the bacterial and fungal community structures differed between VC and AC. The quality of the green waste compost product was higher with VC than with AC. These results will also help to achieve further composting technology breakthroughs in reducing the composting time and improving compost quality.

Microbial community composition of a household sand filter used for arsenic, iron, and manganese removal from groundwater in Vietnam.

Household sand filters are used in rural areas of Vietnam to remove As, Fe, and Mn from groundwater for drinking water purposes. Currently, it is unknown what role microbial processes play in mineral oxide formation and As removal during water filtration. We performed most probable number counts to quantify the abundance of physiological groups of microorganisms capable of catalyzing Fe- and Mn-redox transformation processes in a household sand filter. We found up to 10(4) cells g(-1) dry sand of nitrate-reducing Fe(II)-oxidizing bacteria and Fe(III)-reducing bacteria, and no microaerophilic Fe(II)-oxidizing bacteria, but up to 10(6) cells g(-1) dry sand Mn-oxidizing bacteria. 16S rRNA gene amplicon sequencing confirmed MPN counts insofar as only low abundances of known taxa capable of performing Fe- and Mn-redox transformations were detected. Instead the microbial community on the sand filter was dominated by nitrifying microorganisms, e.g. Nitrospira, Nitrosomonadales, and an archaeal OTU affiliated to Candidatus Nitrososphaera. Quantitative PCR for Nitrospira and ammonia monooxygenase genes agreed with DNA sequencing results underlining the numerical importance of nitrifiers in the sand filter. Based on our analysis of the microbial community composition and previous studies on the solid phase chemistry of sand filters we conclude that abiotic Fe(II) oxidation processes prevail over biotic Fe(II) oxidation on the filter. Yet, Mn-oxidizing bacteria play an important role for Mn(II) oxidation and Mn(III/IV) oxide precipitation in a distinct layer of the sand filter. The formation of Mn(III/IV) oxides contributes to abiotic As(III) oxidation and immobilization of As(V) by sorption to Fe(III) (oxyhydr)oxides.

Differential photoinhibition of bacterial and archaeal ammonia oxidation.

Inhibition by light potentially influences the distribution of ammonia oxidizers in aquatic environments and is one explanation for nitrite maxima near the base of the euphotic zone of oceanic waters. Previous studies of photoinhibition have been restricted to bacterial ammonia oxidizers, rather than archaeal ammonia oxidizers, which dominate in marine environments. To compare the photoinhibition of bacterial and archaeal ammonia oxidizers, specific growth rates of two ammonia-oxidizing archaea (Nitrosopumilus maritimus and Nitrosotalea devanaterra) and bacteria (Nitrosomonas europaea and Nitrosospira multiformis) were determined at different light intensities under continuous illumination and light/dark cycles. All strains were inhibited by continuous illumination at the highest intensity (500 µE m(-2) s(-1)). At lower light intensities, archaeal growth was much more photosensitive than bacterial growth, with greater inhibition at 60 µE m(-2) s(-1) than at 15 µE m(-2) s(-1), where bacteria were unaffected. Archaeal ammonia oxidizers were also more sensitive to cycles of 8-h light/16-h darkness at two light intensities (60 and 15 µE m(-2) s(-1)) and, unlike bacterial strains, showed no evidence of recovery during dark phases. The findings provide evidence for niche differentiation in aquatic environments and reduce support for photoinhibition as an explanation of nitrite maxima in the ocean.

Nitrifying bacterial growth inhibition in the presence of algae and cyanobacteria.

Nitrifying bacteria, cyanobacteria, and algae are important microorganisms in open pond wastewater treatment systems. Nitrification involving the sequential oxidation of ammonia to nitrite and nitrate, mainly due to autotrophic nitrifying bacteria, is essential to biological nitrogen removal in wastewater and global nitrogen cycling. A continuous flow autotrophic bioreactor was initially designed for nitrifying bacterial growth only. In the presence of cyanobacteria and algae, we monitored both the microbial activity by measuring specific oxygen production rate (SOPR) for microalgae and cyanobacteria and specific oxygen uptake rate (SOUR) for nitrifying bacteria. The growth of cyanobacteria and algae inhibited the maximum nitrification rate by a factor of 4 although the ammonium nitrogen fed to the reactor was almost completely removed. Terminal restriction fragment length polymorphism (T-RFLP) analysis indicated that the community structures of nitrifying bacteria remained unchanged, containing the dominant Nitrosospira, Nitrospira, and Nitrobacter species. PCR amplification coupled with cloning and sequencing analysis resulted in identifying Chlorella emersonii and an uncultured cyanobacterium as the dominant species in the autotrophic bioreactor. Notwithstanding their fast growth rate and their toxicity to nitrifiers, microalgae and cyanobacteria were more easily lost in effluent than nitrifying bacteria because of their poor settling characteristics. The microorganisms were able to grow together in the bioreactor with constant individual biomass fractions because of the uncoupled solids retention times for algae/cyanobacteria and nitrifiers. The results indicate that compared to conventional wastewater treatment systems, longer solids retention times (e.g., by a factor of 4) should be considered in phototrophic bioreactors for complete nitrification and nitrogen removal.

Molecular biological characterization and biostimulation of ammonia-oxidizing bacteria in brackishwater aquaculture.

In the present study, molecular methods based on sequencing of clone libraries have been used to provide sequence and the phylogenetic information of ammonia oxidizing bacteria (AOB). Ammonia monooxygenase (amoA) gene, which catalyzed the oxidation of ammonia to hydroxyl amine in the initial rate-determining step of nitrification was targeted for detection and characterization of AOB using gene-specific primers. The amoA genes obtained through the clone library construction are closely affiliated with Nitrosomonas sp. and other uncultured beta proteobacteria. The levels of nucleotide similarity and amino acid similarity ranged from 85-99% and 83-88%, respectively. The level of conservation of the amino acid sequences is 73%. The use of a matrix prepared from abundantly available lignocellulosic agrowaste-bagasse has successfully been demonstrated for biostimulation of AOB in aquaculture environment by supplementing nutritional requirement facilitating the biofilm mode of growth of the autotrophic consortia. Present study is useful in predictability and reliability of the treatment of ammonia in brackishwater aquaculture.

Insitu bioaugmentation of nitrification in the regeneration zone: practical application and experiences at full-scale plants.

Nitrification is the rate-limiting process in the design of activated sludge process. It is especially unstable during the winter season (when the temperature of activated sludge mixed liquor drops below 13 degrees C). It is therefore difficult to meet the ammonia effluent standards in winter. The common way to compensate for low nitrification rates at low temperatures is to increase sludge retention time (SRT). However, the increase of SRT is accompanied by negative factors such as elevated sludge concentration, higher sludge loading of secondary clarifiers, formation of unsettleable microflocs, etc. The low performance of nitrification at low temperatures can also be compensated for by enhancing the nitrification population in activated sludge. This paper describes such a method called bioaugmentation of nitrification in situ. This procedure takes place in a so-called regeneration tank, which is situated in the return activated sludge stream. The results of the operation of two wastewater treatment plants with regeneration zones are described in this paper, together with some economic evaluation of the bioaugmentation method.

Nitrosospira spp. can produce nitrous oxide via a nitrifier denitrification pathway.

Nitrous oxide (N(2)O) emission from soils is a major contributor to the atmospheric loading of this potent greenhouse gas. It is thought that autotrophic ammonia oxidizing bacteria (AOB) are a significant source of soil-derived N(2)O and a denitrification pathway (i.e. reduction of NO(2) (-) to NO and N(2)O), so-called nitrifier denitrification, has been demonstrated as a N(2)O production mechanism in Nitrosomonas europaea. It is thought that Nitrosospira spp. are the dominant AOB in soil, but little information is available on their ability to produce N(2)O or on the existence of a nitrifier denitrification pathway in this lineage. This study aims to characterize N(2)O production and nitrifier denitrification in seven strains of AOB representative of clusters 0, 2 and 3 in the cultured Nitrosospira lineage. Nitrosomonas europaea ATCC 19718 and ATCC 25978 were analysed for comparison. The aerobically incubated test strains produced significant (P < 0.001) amounts of N(2)O and total N(2)O production rates ranged from 2.0 amol cell(-1) h(-1), in Nitrosospira tenuis strain NV12, to 58.0 amol cell(-1) h(-1), in N. europaea ATCC 19718. Nitrosomonas europaea ATCC 19718 was atypical in that it produced four times more N(2)O than the next highest producing strain. All AOB tested were able to carry out nitrifier denitrification under aerobic conditions, as determined by production of (15)N-N(2)O from applied (15)N-NO(2) (-). Up to 13.5% of the N(2)O produced was derived from the exogenously applied (15)N-NO(2) (-). The results suggest that nitrifier denitrification could be a universal trait in the betaproteobacterial AOB and its potential ecological significance is discussed.

In situ substrate conversion and assimilation by nitrifying bacteria in a model biofilm.

Local nitrification and carbon assimilation activities were studied in situ in a model biofilm to investigate carbon yields and contribution of distinct populations to these activities. Immobilized microcolonies (related to Nitrosomonas europaea/eutropha, Nitrosomonas oligotropha, Nitrospira sp., and to other Bacteria) were incubated with [14C]-bicarbonate under different experimental conditions. Nitrifying activity was measured concomitantly with microsensors (oxygen, ammonium, nitrite, nitrate). Biofilm thin sections were subjected to fluorescence in situ hybridization (FISH), microautoradiography (MAR), and local quantification of [14C]-bicarbonate uptake (beta microimaging). Nitrifying activity and tracer assimilation were restricted to a surface layer of different thickness in the various experiments (substrate or oxygen limitation). Excess oxygen uptake under all conditions revealed heterotrophic activity fuelled by decay or excretion products during active nitrification. Depth limits and intensity of tracer incorporation profiles were in agreement with ammonia-oxidation activity (measured with microsensors), and distribution of incorporated tracer (detected with MAR). Microautoradiography revealed a sharp individual response of distinct populations in terms of in-/activity depending on the (local) environmental conditions within the biofilm. Net in situ carbon yields on N, expressed as e- equivalent ratios, varied between 0.005 and 0.018, and, thus, were in the lower range of data reported for pure cultures of nitrifiers.

Links between ammonia oxidizer species composition, functional diversity and nitrification kinetics in grassland soils.

Molecular approaches have revealed considerable diversity and uncultured novelty in natural prokaryotic populations, but not direct links between the new genotypes detected and ecosystem processes. Here we describe the influence of the structure of communities of ammonia-oxidizing bacteria on nitrogen cycling in microcosms containing natural and managed grasslands and amended with artificial sheep urine, a major factor determining local ammonia concentrations in these environments. Nitrification kinetics were assessed by analysis of changes in urea, ammonia, nitrite and nitrate concentrations and ammonia oxidizer communities were characterized by analysis of 16S rRNA genes amplified from extracted DNA using ammonia oxidizer-specific primers. In natural soils, ammonia oxidizer community structure determined the delay preceding nitrification, which depended on the relative abundance of two Nitrosospira clusters, termed 3a and 3b. In batch cultures, pure culture and enrichment culture representatives of Nitrosospira 3a were sensitive to high ammonia concentration, while Nitrosospira cluster 3b representatives and Nitrosomonas europaea were tolerant. Delays in nitrification occurred in natural soils dominated by Nitrosospira cluster 3a and resulted from the time required for growth of low concentrations of Nitrosospira cluster 3b. In microcosms dominated by Nitrosospira cluster 3b and Nitrosomonas, no substantial delays were observed. In managed soils, no delays in nitrification were detected, regardless of initial ammonia oxidizer community structure, most probably resulting from higher ammonia oxidizer cell concentrations. The data therefore demonstrate a direct link between bacterial community structure, physiological diversity and ecosystem function.

Emergence of competitive dominant ammonia-oxidizing bacterial populations in a full-scale industrial wastewater treatment plant.

Ammonia-oxidizing bacterial populations in an industrial wastewater treatment plant were investigated with amoA and 16S rRNA gene real-time PCR assays. Nitrosomonas nitrosa initially dominated, but over time RI-27-type ammonia oxidizers, also within the Nitrosomonas communis lineage, increased from below detection to codominance. This shift occurred even though nitrification remained constant.

Acetylene and oxygen as inhibitors of nitrous oxide production in Nitrosomonas europaea and Nitrosospira briensis: a cautionary tale.

Autotrophic ammonia-oxidizing bacteria produce nitrous oxide (N(2)O) as a by-product of nitrification or as an intermediate of nitrifier denitrification. In soil incubations, acetylene (C(2)H(2)) and large partial pressures of oxygen (O(2)) are used to distinguish between these sources. C(2)H(2) inhibits ammonia oxidation and should therefore inhibit N(2)O production by both nitrification and nitrifier denitrification. O(2) suppresses the reduction pathway of nitrifier denitrification. However, doubts concerning the reliability of C(2)H(2) and O(2) as inhibitors have arisen recently. Therefore, in this study we tested the influence of C(2)H(2) and large partial pressures of O(2) alone and in combination on N(2)O production in pure cultures of the ammonia oxidizers Nitrosomonas europaea and Nitrosospira briensis. C(2)H(2) largely inhibited nitrite production in both ammonia oxidizers and N(2)O production by N. europaea. Surprisingly, it did not affect the N(2)O production in N. briensis. The variable response of ammonia oxidizers to C(2)H(2) might have consequences for the use of C(2)H(2) as an inhibitor of nitrification in soils. Different partial pressures of O(2) ranging from less than 10 kPa O(2) to 100 kPa O(2) were tested for their effectiveness in inhibiting N(2)O production via nitrifier denitrification. The partial pressure of 100 kPa O(2) yielded minimal N(2)O production by both ammonia-oxidizing species and seemed to inhibit N(2)O emission from nitrifier denitrification to a large extent. However, a negative effect of 100 kPa O(2) on ammonia oxidation itself could not be excluded. The applicability of both inhibitors in determining N(2)O production pathways in soils is discussed.

A comparitive study of ammonia-oxidizing bacteria in lab-scale industrial wastewater treatment reactors.

The diversity and community structure of the beta-proteobacterial ammonia oxidising bacteria (AOB) in a range of different lab-scale industrial wastewater treatment reactors were compared. Three of the reactors treat waste from mixed domestic and industrial sources whereas the other reactor treats waste solely of industrial origin. PCR with AOB selective primers was combined with denaturing gradient ge electrophoresis to allow comparative analysis of the dominant AOB populations and the phylogenetic affiliation of the dominant AOB was determined by cloning and sequencing or direct sequencing of bands excised from DGGE gels. Different AOB were found within and between different reactors. All AOB sequences identified were grouped within the genus Nitrosomonas. Within the lab-scale reactors there appeared to be selection for a low diversity of AOB and predominance of a single AOB population. Furthermore, the industrial input in both effluents apparently selected for salt tolerant AOB, most closely related to Nitrosococcus mobilis and Nitrosomonas halophila.