Isolation and identification of nitrifying bacteria from tilapia (Oreochromis sp.) pond in Sleman Yogyakarta Indonesia

This research aims to isolate and identify autochtonous nitrifying bacteria from tilapia pond in Sleman Yogyakarta Indonesia for future application in aquaculture practices in the region. Bacteria were isolated using a nitrification medium. Bacterial characterization was carried out by non-pathogenic test to tilapia (Oreochromis sp.), and nitrification activity test in a single bacterial fermentation medium for 9 days. Bacterial identification was carried out based on the colony and cell morphologies, biochemical tests, and molecular analysis using the 16S rRNA and gyrB genes. A total of 15 isolates of nitrifying bacteria were obtained. Four non-pathogenic isolates obtained the highest nitrification activity on the sixth day of incubation, with nitrate production of 17.26-21.54 ppm. Two selected bacteria, isolates A2 and A3, have colony morphology that is milky white, smooth surface, circular shape, entire edge, and convex elevation. Both bacteria are short rods, Gram-negative, non-motile, produce catalase, fermenting glucose, sucrose, and lactose, and do not produce oxidase, ornithine decarboxylase, indole, and H2S. Molecular analysis showed that the two isolates had the highest similarity (99.28% and 99.34%) to Klebsiella spp.

Soil Amendments Alter Ammonia-Oxidizing Archaea and Bacteria Communities in Rain-Fed Maize Field in Semi-Arid Loess Plateau

Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are key drivers of nitrification in rainfed soil ecosystems. However, within a semi-arid region, the influence of different soil amendments on the composition of soil AOA and AOB communities and soil properties of rainfed maize is still unclear. Therefore, in this study, the abundance, diversity, and composition of AOA and AOB communities and the potential nitrification activity (PNA) was investigated across five soil treatments: no fertilization (NA), urea fertilizer (CF), cow manure (SM), corn stalk (MS), and cow manure + urea fertilizer (SC). The AOB amoA gene copy number was influenced significantly by fertilization treatments. The AOB community was dominated by Nitrosospira cluster 3b under the CF and SC treatments, and the AOA community was dominated by Nitrososphaera Group I.1b under the CF and NA amendments; however, manure treatments (SM, MS, and SC) did not exhibit such influence. Network analysis revealed the positive impact of some hub taxonomy on the abundance of ammonia oxidizers. Soil pH, NO3−-N, Module 3, biomass, and AOB abundance were the major variables that influenced the potential nitrification activity (PNA) within structural equation modeling. PNA increased by 142.98–226.5% under the treatments CF, SC, SM, and MS compared to NA. In contrast to AOA, AOB contributed dominantly to PNA. Our study highlights the crucial role of bacterial communities in promoting sustainable agricultural production in calcareous soils in semi-arid loess plateau environments.

Spatiotemporal evolution and assembly processes of ammonia-oxidising prokaryotic communities in 1000 years coastal reclaimed soils

Coastal marshes are transitional areas between terrestrial and aquatic ecosystems and vulnerable to climate change and anthropogenic activities. In recent decades the reclamation of coastal marshes remarkably increased and their effects on microbial communities present in coastal marshes have been studied with great interest. However, most of these studies focused on microbial community composition and diversity. The processes underlying functional community assembly and spatiotemporal effect often ignored. Therefore, community structure and assembly mechanisms of ammonia-oxidising prokaryotes in long-term reclaimed coastal marshes have not been studied. Here using qPCR and IonS5TMXL sequencing platform, we investigated spatiotemporal dynamics, assembly processes and diversity patterns in ammonia-oxidising prokaryotes in over 1000 years reclaimed coastal salt marsh soils. The taxonomic & phylogenetic diversity and composition of the ammonia-oxidizers showed apparent spatiotemporal variations along reclamation of soil. The phylogenetic null modelling-based analysis showed across all sites, the archaeal ammonia-oxidising community assembled by deterministic process (84.71%). The ammonia-oxidising bacterial community was formed more by a stochastic process in coastal marshes and at stage 60 years (|βNTI|<2), despite its relatively dominant deterministic process (55.2%). The deterministic assembly process and nitrification activity in reclaimed soils was positively correlated. Archaeal amoA gene abundance were also positively correlated with the nitrification rate. Our study revealed that during the 1000 years of reclamation coastal marshes both ammonia-oxidising communities responded differently to diversity change and assembly processes and nitrification activity. These findings provide a better understanding of how long-term reclamation affect soil N cycling and assembly dynamics of ammonia-oxidising communities.

Microbially facilitated nitrogen cycling in tropical corals

Tropical scleractinian corals support a diverse assemblage of microbial symbionts. This ‘microbiome’ possesses the requisite functional diversity to conduct a range of nitrogen (N) transformations including denitrification, nitrification, nitrogen fixation and dissimilatory nitrate reduction to ammonium (DNRA). Very little direct evidence has been presented to date verifying that these processes are active within tropical corals. Here we use a combination of stable isotope techniques, nutrient uptake calculations and captured metagenomics to quantify rates of nitrogen cycling processes in a selection of tropical scleractinian corals. Denitrification activity was detected in all species, albeit with very low rates, signifying limited importance in holobiont N removal. Relatively greater nitrogen fixation activity confirms that corals are net N importers to reef systems. Low net nitrification activity suggests limited N regeneration capacity; however substantial gross nitrification activity may be concealed through nitrate consumption. Based on nrfA gene abundance and measured inorganic N fluxes, we calculated significant DNRA activity in the studied corals, which has important implications for coral reef N cycling and warrants more targeted investigation. Through the quantification and characterisation of all relevant N-cycling processes, this study provides clarity on the subject of tropical coral-associated biogeochemical N-cycling.

Effect of antibiotics on the cellulolytic and nitrification activity of gray forest soil

Aim. To investigate the effect of certain antibiotics - tylosin, oxytetracycline and benzylpenicillin - on the potential nitrifying and cellulolytic activity of gray forest soil using laboratory model research methods.Material and Methods. The object of the research was agricultural gray forest medium loamy soil. The study was carried out by conducting laboratory model experiments. The analysed samples were incubated at 27°C and in the absence of illumination for 30 days and then subsequently analysed for cellulolytic activity (by the application method) and nitrification activity (by the potentiometric method). The taxonomic composition of the bacterial community of the studied soil was established based on analysis of amplicon libraries of fragments of ribosomal operons of 16S rRNA genes by the NGS method.Results. The largest number of nitrification organisms in the soil studied were archaea of the family Nitrososphaeraceae which are autotrophic ammonium oxidants. Most resistant to the effects of the antibiotics used was cellulolytic activity which was suppressed only by the addition of tylosin and its admixture with oxytetracycline. The nitrification activity of the soil varied depending on the concentration and preparations applied, the greatest inhibitory effect being exerted by tylosin. Antibiotic mixtures slightly enhanced the nitrification process at 50-100 mg/kg and were suppressed in the range of 150-700 mg/kg. Conclusion. Once in the soil, the antibiotics studied are capable of both stimulating and inhibiting enzymatic processes. Mixtures of antibiotics rather than their individual applications produce the greatest impact. In medium loamy gray forest soil the presence of antibiotics is more dangerous to nitrification activity.

Nitrification Activity of the Sponge Chondrosia reniformis Under Elevated Concentrations of Ammonium

This study examined the ability of a Mediterranean demosponge Chondrosia reniformis to oxidize exogenous ammonium, simulating N-rich conditions that occur near finfish farms. We hypothesized that as the concentration of ammonium increases in the surrounding seawater, nitrification mediated by microbes associated with C. reniformis will lead to enhancement of ammonium uptake, nitrate excretion and oxygen consumption by the sponge holobiont. To test this hypothesis, we conducted laboratory experiments with C. reniformis explants exposed to ammonium enrichments (300–6667 nM) and to ambient seawater (45–1511 nM ammonium). We analyzed inhaled (IN) and exhaled (EX) water samples for dissolved oxygen, ammonium, nitrates and retention of picoplankton cells. We observed ammonium uptake in nearly half the cases and excretion of nitrate in most experimental outcomes. Yet, the consumption of ammonium and oxygen, as well as the excretion of nitrate by C. reniformis were not related to the concentration of inhaled ammonium, which suggests that the nitrification activity of sponge-associated microbes is not necessarily related to the concentration of ammonium in the surrounding seawater. Further research is required to reveal the sources of nitrate released from sponges and the fate of this nitrate in natural and manipulated ecosystems.

A history of extreme disturbance affects the relationship between the abundances of nitrifiers in soil

To understand how and to what extent single or multiple perturbations can alter the relationships between the abundances of different nitrifier groups and nitrification, soil microcosms were exposed to six disturbance treatments: a heat shock, cold shock, or control conditions applied to undisturbed soils or to soils that had previously been subjected to a first heat shock. We monitored the recovery of the abundances of four main nitrifier groups (ammonia-oxidizing archaea and bacteria, AOA and AOB, respectively, and Nitrobacter and Nitrospira nitrite oxidizers) as well as nitrification activity for 25 days. AOA were sensitive to cold shocks, whereas AOB were not; the latter were sensitive to heat shock. Despite the variations, both groups were resilient to the first disturbance. In contrast, Nitrobacter was affected by both disturbances, whereas Nitrospira was resistant to both shocks. Prior exposure to a heat shock affected each group’s responses as well as the relationships between them. For example, AOB were more vulnerable to heat shock in pre-exposed soils, whereas under the same circumstances, AOA were resilient. Nitrification activity was resistant to the first disturbances, but a legacy effect was observed, and nitrification was highest in Heat-Heat and lowest in Heat-Cold treatments. Overall, our study shows that within soil nitrifiers, temporal patterns and legacy effects interact to result in complex disturbance responses.