Estuarine Nitrifiers: New Players, Patterns and Processes

Ever since the first descriptions of ammonia-oxidizing Bacteria by Winogradsky in the late 1800s, the metabolic capability of aerobic ammonia oxidation has been restricted to a phylogenetically narrow group of bacteria. However, the recent discovery of ammonia-oxidizing Archaea has forced microbiologists and ecologists to re-evaluate long-held paradigms and the role of niche partitioning between bacterial and archaeal ammonia oxidizers. Much of the current research has been conducted in open ocean or terrestrial systems, where community patterns of archaeal and bacterial ammonia oxidizers are highly congruent. Studies of archaeal and bacterial ammonia oxidizers in estuarine systems, however, present a very different picture, with highly variable patterns of archaeal and bacterial ammonia oxidizer abundances. Although salinity is often identified as an important factor regulating abundance, distribution, and diversity of both archaeal and bacterial ammonia oxidizers, the data suggest that the variability in the observed patterns is likely not due to a simple salinity effect. Here we review current knowledge of ammonia oxidizers in estuaries and propose that because of their steep physico-chemical gradients, estuaries may serve as important natural laboratories in which to investigate the relationships between archaeal and bacterial ammonia oxidizers

ВИКОРИСТАННЯ ІМПУЛЬСНОГО МЕТОДУ ВИМІРЮВАННЬ ДЛЯ ВИЗНАЧЕННЯ ПОШКОДЖЕННЯ КАБЕЛЬНИХ ЛІНІЙ

В даній роботі розглядаються особливості використання приладу ІКЛ-5 для швидкого визначення точності імпульсних вимірювань в пошкодженнях кабельних ліній і точного знаходження міста пошкодження кабелю. Для досягнення поставленої мети запропонований імпульсний метод, який визначає місце і характер пошкодження кабельних ліній. Обраний у роботі підхід дає можливість вимірювання при будьякому складному характері ушкодження. Завдяки цьому забезпечується зручність, простота і швидкість вимірювань

Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea

Ammonia-oxidizing archaea (AOA) are among the most abundant and ubiquitous microorganisms in the ocean, exerting primary control on nitrification and nitrogen oxides emission. Although united by a common physiology of chemoautotrophic growth on ammonia, a corresponding high genomic and habitat variability suggests tremendous adaptive capacity. Here, we compared 44 diverse AOA genomes, 37 from species cultivated from samples collected across diverse geographic locations and seven assembled from metagenomic sequences from the mesopelagic to hadopelagic zones of the deep ocean. Comparative analysis identified seven major marine AOA genotypic groups having gene content correlated with their distinctive biogeographies. Phosphorus and ammonia availabilities as well as hydrostatic pressure were identified as selective forces driving marine AOA genotypic and gene content variability in different oceanic regions. Notably, AOA methylphosphonate biosynthetic genes span diverse oceanic provinces, reinforcing their importance for methane production in the ocean. Together, our combined comparative physiological, genomic, and metagenomic analyses provide a comprehensive view of the biogeography of globally abundant AOA and their adaptive radiation into a vast range of marine and terrestrial habitats

Genome Sequence of Nitrosomonas sp. Strain AL212, an Ammonia-Oxidizing Bacterium Sensitive to High Levels of Ammonia

Nitrosomonas sp. strain AL212 is an obligate chemolithotrophic ammonia-oxidizing bacterium (AOB) that was originally isolated in 1997 by Yuichi Suwa and colleagues. This organism belongs to Nitrosomonas cluster 6A, which is characterized by sensitivity to high ammonia concentrations, higher substrate affinity (lower K[subscript m]), and lower maximum growth rates than strains in Nitrosomonas cluster 7, which includes Nitrosomonas europaea and Nitrosomonas eutropha. Genome-informed studies of this ammonia-sensitive cohort of AOB are needed, as these bacteria are found in freshwater environments, drinking water supplies, wastewater treatment systems, and soils worldwide

Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations

Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia oxidation is the first step of nitrification, an important process in the global nitrogen cycle ultimately resulting in the production of nitrate. Nitrosomonas sp. Is79 is an ammonia oxidizer of high interest because it is adapted to low ammonium and can be found in freshwater environments around the world. The 3,783,444-bp chromosome with a total of 3,553 protein coding genes and 44 RNA genes was sequenced by the DOE-Joint Genome Institute Program CSP 2006.Keywords: nitrification, Ammonia-oxidizing bacteria, Ammonia oxidation, Nitrosomonas, nitrogen cycle, oligotrophic, freshwate

Freshwater Ammonia-Oxidizing Archaea Retain amoA mRNA and 16S rRNA during Ammonia Starvation

In their natural habitats, microorganisms are often exposed to periods of starvation if their substrates for energy generation or other nutrients are limiting. Many microorganisms have developed strategies to adapt to fluctuating nutrients and long-term starvation. In the environment, ammonia oxidizers have to compete with many different organisms for ammonium and are often exposed to long periods of ammonium starvation. We investigated the effect of ammonium starvation on ammonia-oxidizing archaea (AOA) and bacteria (AOB) enriched from freshwater lake sediments. Both AOA and AOB were able to recover even after almost two months of starvation; however, the recovery time differed. AOA and AOB retained their 16S rRNA (ribosomes) throughout the complete starvation period. The AOA retained also a small portion of the mRNA of the ammonia monooxygenase subunit A (amoA) for the complete starvation period. However, after 10 days, no amoA mRNA was detected anymore in the AOB. These results indicate that AOA and AOB are able to survive longer periods of starvation, but might utilize different strategies

Incubation of Environmental Samples in a Diffusion Chamber Increases the Diversity of Recovered Isolates▿ †

The majority of microorganisms from natural environments cannot be grown in the laboratory. The diffusion-chamber-based approach is an alternative method that allows microorganisms to grow in their natural environment. An inoculum is sandwiched between semipermeable (0.03-μm-pore-size) membranes of the chamber, which is then returned to the source environment. The chamber allows for a free exchange of chemicals with the external milieu by diffusion while restricting the movement of cells. We used freshwater pond sediment to inoculate diffusion chambers and petri dishes. The diffusion chambers were incubated on top of the sediment for 4 weeks. Both chamber and petri dish cultivation resulted in the isolation of numerous representatives of Alpha-, Beta-, and Gammaproteobacteria; Actinobacteria; Firmicutes; and Bacteroidetes. However, the diffusion-chamber-based approach also led to the isolation of species from rarely cultivated groups, such as Deltaproteobacteria, Verrucomicrobia, Spirochaetes, and Acidobacteria. Material from the chambers was also transferred to new chambers in order to learn whether this will increase the recovery of isolates. Several isolates could be obtained only from material transferred through multiple diffusion chambers. This suggests that continuous cultivation in diffusion chambers adapts some microorganisms for growth under otherwise prohibitive in vitro conditions

Physiological and Genomic Characterization of Two Novel Bacteroidota Strains Asinibacterium spp. OR43 and OR53

Asinibacterium spp. (Family Chitinophagaceae, Phylum Bacteroidota) are abundant in environments contaminated with heavy metals. We characterized the physiology and genome of two Asinibacterium species to elucidate their ability to survive and grow at ambient conditions in the uranium-contaminated environments. Both strains were able to grow at pH 4.5 or 50 mM nitrate under aerobic conditions and did not grow with alternative electron acceptors under anaerobic conditions. Asinibacterium sp. OR53 grew in medium with uranium concentrations up to 300 µM uranium while Asinibacterium sp. OR43 could not grow at uranium concentrations > 200 µM. Elemental mapping using energy dispersive X-ray spectroscopy indicate that uranium co-localized with phosphorus-containing compounds on the cell surface. Genes potentially encoding resistance mechanisms to a variety of heavy metals were detected in the genomes of both strains. The localization of uranium and missing acidic and alkaline phosphatase genes in the genome suggest that biosorption of uranium to the lipopolysaccharide layer might be the mechanism of uranium resistance. In summary, Asinibacterium spp. OR43 and OR53 are physiologically similar to closely related strains within the Chitinophagaceae family but are uniquely acclimated to the presence of uranium and other heavy metals prevalent in the subsurface at Oak Ridge, Tennessee