Nitrosospira lacus sp. nov., a psychrotolerant, ammonia-oxidizing bacterium from sandy lake sediment

A Gram-negative, spiral-shaped, chemolithotrophic, ammonia-oxidizing bacterium, designated APG3T, was isolated into pure culture from sandy lake sediment collected from Green Lake, Seattle, WA, USA. Phylogenetic analyses based on the 16S rRNA gene sequence showed that strain APG3T belongs to cluster 0 of the genus Nitrosospira , which is presently not represented by described species, with Nitrosospira multiformis (cluster 3) as the closest species with a validly published name (identity of 98.6 % to the type strain). Strain APG3T grew at 4 °C but could not grow at 35 °C, indicating that this bacterium is psychrotolerant. Remarkably, the strain was able to grow over a wide range of pH (pH 5–9), which was greater than the pH range of any studied ammonia-oxidizing bacteria in pure culture. The DNA G+C content of the APG3T genome is 53.5 %, which is similar to that of Nitrosospira multiformis ATCC 25196T (53.9 %) but higher than that of Nitrosomonas europaea ATCC 19718 (50.7 %) and Nitrosomonas eutropha C71 (48.5 %). The average nucleotide identity (ANI) calculated for the genomes of strain APG3T and Nitrosospira multiformis ATCC 25196T was 75.45 %, significantly lower than the value of 95 % ANI that corresponds to the 70 % species-level cut-off based on DNA–DNA hybridization. Overall polyphasic taxonomy study indicated that strain APG3T represents a novel species in the genus Nitrosospira , for which the name Nitrosospira lacus sp. nov. is proposed (type strain APG3T = NCIMB 14869T = LMG 27536T = ATCC BAA-2542T).</jats:p

Hydroxylamine released by nitrifying microorganisms is a precursor for HONO emission from drying soils

Abstract Nitrous acid (HONO) is an important precursor of the hydroxyl radical (OH), the atmosphere´s primary oxidant. An unknown strong daytime source of HONO is required to explain measurements in ambient air. Emissions from soils are one of the potential sources. Ammonia-oxidizing bacteria (AOB) have been identified as possible producers of these HONO soil emissions. However, the mechanisms for production and release of HONO in soils are not fully understood. In this study, we used a dynamic soil-chamber system to provide direct evidence that gaseous emissions from nitrifying pure cultures contain hydroxylamine (NH2OH), which is subsequently converted to HONO in a heterogeneous reaction with water vapor on glass bead surfaces. In addition to different AOB species, we found release of HONO also in ammonia-oxidizing archaea (AOA), suggesting that these globally abundant microbes may also contribute to the formation of atmospheric HONO and consequently OH. Since biogenic NH2OH is formed by diverse organisms, such as AOB, AOA, methane-oxidizing bacteria, heterotrophic nitrifiers, and fungi, we argue that HONO emission from soil is not restricted to the nitrifying bacteria, but is also promoted by nitrifying members of the domains Archaea and Eukarya

HONO Emissions from Soil Bacteria as a Major Source of Atmospheric Reactive Nitrogen

International audienceAbiotic release of nitrous acid (HONO) in equilibrium with soil nitrite (NO2-) was suggested as an important contributor to the missing source of atmospheric HONO and hydroxyl radicals (OH). The role of total soil-derived HONO in the biogeochemical and atmospheric nitrogen cycles, however, has remained unknown. In laboratory experiments, we found that for nonacidic soils from arid and arable areas, reactive nitrogen emitted as HONO is comparable with emissions of nitric oxide (NO). We show that ammonia-oxidizing bacteria can directly release HONO in quantities larger than expected from the acid-base and Henry's law equilibria of the aqueous phase in soil. This component of the nitrogen cycle constitutes an additional loss term for fixed nitrogen in soils and a source for reactive nitrogen in the atmosphere

Identification of Bacteria Responsible for Ammonia Oxidation in Freshwater Aquaria

Culture enrichments and culture-independent molecular methods were employed to identify and confirm the presence of novel ammonia-oxidizing bacteria (AOB) in nitrifying freshwater aquaria. Reactors were seeded with biomass from freshwater nitrifying systems and enriched for AOB under various conditions of ammonia concentration. Surveys of cloned rRNA genes from the enrichments revealed four major strains of AOB which were phylogenetically related to the Nitrosomonas marina cluster, the Nitrosospira cluster, or the Nitrosomonas europaea-Nitrosococcus mobilis cluster of the β subdivision of the class Proteobacteria. Ammonia concentration in the reactors determined which AOB strain dominated in an enrichment. Oligonucleotide probes and PCR primer sets specific for the four AOB strains were developed and used to confirm the presence of the AOB strains in the enrichments. Enrichments of the AOB strains were added to newly established aquaria to determine their ability to accelerate the establishment of ammonia oxidation. Enrichments containing the Nitrosomonas marina-like AOB strain were most efficient at accelerating ammonia oxidation in newly established aquaria. Furthermore, if the Nitrosomonas marina-like AOB strain was present in the original enrichment, even one with other AOB, only the Nitrosomonas marina-like AOB strain was present in aquaria after nitrification was established. Nitrosomonas marina-like AOB were 2% or less of the cells detected by fluorescence in situ hybridization analysis in aquaria in which nitrification was well established

Nutritional and Possible Pharmaceutical Aspects of Tree Exudates Eaten by Lemurs of Madagascar’s Dry Forests

Gums produced by trees after injuries are valuable food resources for several primate species. Yet, information on the chemical characteristics of gum is scant and inconsistent. We use gums consumed by lemurs (strepsirrhine primates of Madagascar) as an example to illustrate their possible nutritive and pharmaceutical properties. Exudates from 45 tree species of the dry forests of Madagascar contained 0.38–23.29% protein, 0.46–65.62% sugar, and 0.39–11.86 kJ/g of energy in dry matter. Exemplified by the lemur species Microcebus griseorufus, gum consumption increased with increasing sugar and energy content but was unrelated to protein. But lemurs also fed on gum with very low protein and energy content, suggesting that these exudates were consumed for other reasons. Disk diffusion tests with exudates from five out of 22 tree species consumed by lemurs showed antibacterial activity against Micrococcus spp. and/or Staphylococcus aureus. Exudates with antibacterial activity had lower protein, sugar, and energy contents than samples without antibacterial properties. GC-MS analyses revealed several components with antimicrobial effects that would have the potential for self-medication. This might explain the consumption of gum with very low nutritive value. Possible medicinal effects of tree exudates deserve further attention in view of their pharmaceutical applicability for animals and humans alike

Rhizobium sp. Strain NGR234 Possesses a Remarkable Number of Secretion Systems▿ †

Rhizobium sp. strain NGR234 is a unique alphaproteobacterium (order Rhizobiales) that forms nitrogen-fixing nodules with more legumes than any other microsymbiont. We report here that the 3.93-Mbp chromosome (cNGR234) encodes most functions required for cellular growth. Few essential functions are encoded on the 2.43-Mbp megaplasmid (pNGR234b), and none are present on the second 0.54-Mbp symbiotic plasmid (pNGR234a). Among many striking features, the 6.9-Mbp genome encodes more different secretion systems than any other known rhizobia and probably most known bacteria. Altogether, 132 genes and proteins are linked to secretory processes. Secretion systems identified include general and export pathways, a twin arginine translocase secretion system, six type I transporter genes, one functional and one putative type III system, three type IV attachment systems, and two putative type IV conjugation pili. Type V and VI transporters were not identified, however. NGR234 also carries genes and regulatory networks linked to the metabolism of a wide range of aromatic and nonaromatic compounds. In this way, NGR234 can quickly adapt to changing environmental stimuli in soils, rhizospheres, and plants. Finally, NGR234 carries at least six loci linked to the quenching of quorum-sensing signals, as well as one gene (ngrI) that possibly encodes a novel type of autoinducer I molecule