Sequence analysis of an Archaeal virus isolated from a hypersaline lake in Inner Mongolia, China

<p>Abstract</p> <p>Background</p> <p>We are profoundly ignorant about the diversity of viruses that infect the domain <it>Archaea</it>. Less than 100 have been identified and described and very few of these have had their genomic sequences determined. Here we report the genomic sequence of a previously undescribed archaeal virus.</p> <p>Results</p> <p>Haloarchaeal strains with 16S rRNA gene sequences 98% identical to <it>Halorubrum saccharovorum </it>were isolated from a hypersaline lake in Inner Mongolia. Two lytic viruses infecting these were isolated from the lake water. The BJ1 virus is described in this paper. It has an icosahedral head and tail morphology and most likely a linear double stranded DNA genome exhibiting terminal redundancy. Its genome sequence has 42,271 base pairs with a GC content of ~65 mol%. The genome of BJ1 is predicted to encode 70 ORFs, including one for a tRNA. Fifty of the seventy ORFs had no identity to data base entries; twenty showed sequence identity matches to archaeal viruses and to haloarchaea. ORFs possibly coding for an origin of replication complex, integrase, helicase and structural capsid proteins were identified. Evidence for viral integration was obtained.</p> <p>Conclusion</p> <p>The virus described here has a very low sequence identity to any previously described virus. Fifty of the seventy ORFs could not be annotated in any way based on amino acid identities with sequences already present in the databases. Determining functions for ORFs such as these is probably easier using a simple virus as a model system.</p

Assembly of microbial communities in replicate nutrient-cycling model ecosystems follows divergent trajectories, leading to alternate stable states

We studied in detail the reproducibility of community development in replicate nutrient‐cycling microbial microcosms that were set up identically and allowed to develop under the same environmental conditions. Multiple replicate closed microcosms were constructed using pond sediment and water, enriched with cellulose and sulphate, and allowed to develop over several months under constant environmental conditions, after which their microbial communities were characterized using 16S rRNA gene sequencing. Our results show that initially similar microbial communities can follow alternative – yet stable – trajectories, diverging in time in a system size‐dependent manner. The divergence between replicate communities increased in time and decreased with larger system size. In particular, notable differences emerged in the heterotrophic degrader communities in our microcosms; one group of steady state communities was enriched with Firmicutes, while the other was enriched with Bacteroidetes. The communities dominated by these two phyla also contained distinct populations of sulphate‐reducing bacteria. This biomodality in community composition appeared to arise during recovery from a low‐diversity state that followed initial cellulose degradation and sulphate reduction

Eliciting expert judgements to underpin our understanding of faecal indicator organism loss from septic tank systems

Septic tank systems (STS) in rural catchments represent a potential source of microbial pollution to watercourses; however, data concerning the risk of faecal indicator organism (FIO) export from STS to surface waters are scarce. In the absence of empirical data, elicitation of expert judgements can provide an alternative approach to aid understanding of FIO pollution risk from STS. Our study employed a structured elicitation process using the Sheffield Elicitation Framework to obtain expert judgements on the proportion of FIOs likely to be delivered from STS to watercourses, based on 36 scenarios combining: (i) septic tank effluent movement risk, driven by soil hydro-morphological characteristics; (ii) distance of septic tank to watercourse; and (iii) degree of slope. Experts used the tertile method to elicit a range of values representing their beliefs of the proportion of FIOs likely to be delivered to a watercourse for each scenario. The experts judged that 93 % of FIOs would likely be delivered from an STS to a watercourse under the highest risk scenario that combined (i) very high STS effluent movement risk, (ii) STS distance to watercourse 25 %. Under the lowest risk scenario, the proportion of FIOs reaching a watercourse would likely reduce to 5 %. Expert confidence was high for scenarios that represented extremes of risk, while uncertainty increased for scenarios depicting intermediate risk conditions. The behavioural aggregation process employed to obtain a consensus among the experts proved to be useful for highlighting both areas of strong consensus and high uncertainty. The latter therefore represent priorities for future empirical research to further improve our understanding of potential pollution risk from septic tanks and in turn enable better assessments of potential threats to water quality in rural catchments throughout the world where decentralised wastewater systems are common

Antibiotic resistance patterns in soils across the Scottish landscape

The environment disseminates antimicrobial-resistance genes; however, it remains challenging to distinguish whether human activities exacerbate antimicrobial resistance or what is natural. Here, we quantified ~300 resistance-related genes in 200+ Scottish soil samples. Location or land use does not explain gene differences, but nutrient levels reduce gene richness. Elevated levels of metals increased gene richness, and selenium increased transposase levels. Rainfall and persistent organic pollutants also increased transposase relative abundance, possibly promoting conditions conducive to the horizontal transfer of antimicrobial-resistance genes. Selenium and polychlorinated biphenyls were primary factors in gene abundance, while polychlorinated biphenyls, polycyclic aromatic hydrocarbons, and pH influenced gene diversity. Polychlorinated biphenyls are derived from anthropogenic activities, highlighting human activities’ potential impact on gene prevalence. This is the first national-scale, high spatial resolution dataset of antimicrobial-resistance genes in Scottish soils and provides a novel resource on which to build future studies

Water safety plan enhancements with improved drinking water quality detection techniques

Drinking water quality has been regulated in most European countries for nearly two decades by the drinking water directive 98/83/EC. The directive is now under revision with the goal of meeting stricter demands for safe water for all citizens, as safe water has been recognized as a human right by the United Nations. An important change to the directive is the implementation of a risk-based approach in all regulated water supplies. The European Union Framework Seventh Programme Aquavalens project has developed several new detection technologies for pathogens and indicators and tested them in water supplies in seven European countries. One of the tasks of the project was to evaluate the impact of these new techniques on water safety and on water safety management. Data were collected on risk factors to water safety for five large supplies in Denmark, Germany, Spain and the UK, and for fifteen small water supplies in Scotland, Portugal and Serbia, via a questionnaire aiming to ascertain risk factors and the stage of implementation of Water Safety Plans, and via site-specific surveys known as Sanitary Site Inspection. Samples were collected from the water supplies from all stages of water production to delivery. Pathogens were detected in around 23% of the 470 samples tested. Fecal contamination was high in raw water and even in treated water at the small supplies. Old infrastructure was considered a challenge at all the water supplies. The results showed that some of the technique, if implemented as part of the water safety management, can detect rapidly the most common waterborne pathogens and fecal pollution indicators and therefore have a great early warning potential; can improve water safety for the consumer; can validate whether mitigation methods are working as intended; and can confirm the quality of the water at source and at the tap

Microbial diversity of Chinese lakes

The microbial ecology of hot springs in Rehai geothermal field in Yunnan Province, China and salt lakes in Inner Mongolia, China were investigated. 16S ribosomal RNA (rRNA) genes were amplified from these environments and were cloned and sequenced. This molecular analysis showed that the 72.1'C hot spring contained Aquificae-dominated white streamers, while the hot water discharge (60 - 65*C) contained a laminated mat. This analysis also showed that the salt lakes were dominated by Halorubrum (34% of clone sequences). The salt lakes' bacterial community consisted of Gammaproteobacteria(2 0%), Finnicutes (20%) and Bacteroidetes (20%), though the bacterium Salinibacter ruber appeared to be the predominant bacterium in the saltern at Lake Ejinnor. Moreover, several Gammaproteobacteria (67% of bacterial isolates) and Firmicutes (23%) and a few Archaea (Halorubrum and Haloarcula sp.) were cultivated from the salt lakes; the majority of isolates retrieved were not detected by molecular analysis. Statistical analysis showed that temperature, Na and Mg ions, and pH were the factors that drive microbial community composition in the salt lakes, and that geographic distance is not a factor, hence the hypothesis that 'the milieu selects' can be applicable. Furthermore, the archaeal community consists of closely related lineages, whereas the bacterial community is highly diverse. Two novel archaeal viruses that infect a haloarchaeal strain that is 98% identical to Halontbrian saccharovorum1 6S rRNA sequencew ere isolated from salt lake water of Lake Bagaejinnor. Both are lytic head/tailed viruses; virus BJ1 is assigned to the Siphoviridae, while virus BJ2 is assigned to the Myoviridae, both of the order Caudovirales. Virus BJI has a 42271 base pair (bp) double stranded (ds) DNA genome, with a G+C content of 64.8 mol% that is terminally redundant and may be circularly permuted. Almost all Open Reading Frames (ORFs) are in the forward strand in the same direction consistent with a rolling circle mechanism of DNA replication. A fraction of the virus population contained extra DNA that is probably host derived, and may suggest viral integration. Virus BJ2 genome is linear dsDNA. It is incomplete, but 97602 bp (approximately 90% of the genome) has been sequenced which has a G+C content of 51 mol% in 42 contigs. No genomici dentity between the viruses has been observed. Virus BJ2 has a narrow host range; it is unable to infect the type strain of Halorubrum saccharovorum or closely related field isolates. Virus BJ2 is stable from 4*C to 50'C, but titres drop ten fold at 60'C. Maximal titres were observed at 2 to 3M NaCl and titres were stable at pH 6- 10, but reduced 10000 fold at pH 4

Microbial diversity of Chinese lakes

Additional information available on CD in the print copy held at the University of Leicester Library.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Novel Electrochemically Active Bacterium Phylogenetically Related to Arcobacter butzleri, Isolated from a Microbial Fuel Cell▿ †

Exoelectrogenic bacteria are organisms that can transfer electrons to extracellular insoluble electron acceptors and have the potential to be used in devices such as microbial fuel cells (MFCs). Currently, exoelectrogens have been identified in the Alpha-, Beta-, Gamma- and Deltaproteobacteria, as well as in the Firmicutes and Acidobacteria. Here, we describe use of culture-independent methods to identify two members of the genus Arcobacter in the Epsilonproteobacteria that are selectively enriched in an acetate-fed MFC. One of these organisms, Arcobacter butzleri strain ED-1, associates with the electrode and rapidly generates a strong electronegative potential as a pure culture when it is supplied with acetate. A mixed-community MFC in which ∼90% of the population is comprised of the two Arcobacter species generates a maximal power density of 296 mW/liter. This demonstration of exoelectrogenesis by strain ED-1 is the first time that this property has been shown for members of this genus

Rapid extraction of high- and low-density microplastics from soil using high-gradient magnetic separation.

Microplastics (MPs) are present in all environments, and concerns over their possible detrimental effects on flora and fauna have arisen. Density separation (DS) is commonly used to separate MPs from soils to allow MP quantification; however, it frequently fails to extract high-density MPs sufficiently, resulting in under-estimation of MP abundances. In this proof-of-concept study, a novel three-stage extraction method was developed, involving high-gradient magnetic separation and removal of magnetic soil (Stage 1), magnetic tagging of MPs using surface modified iron nanoparticles (Stage 2), and high-gradient magnetic recovery of surface-modified MPs (Stage 3). The method was optimised for four different soil types (loam, high‑carbon loamy sand, sandy loam and high-clay sandy loam) spiked with different MP types (polyethylene, polyethylene terephthalate, and polytetrafluoroethylene) of different particle sizes (63μm to 2mm) as well as polyethylene fibres (2–4mm). The optimised method achieved average recoveries of 96% for fibres and 92% for particles in loam, 91% for fibres and 87% for particles in high‑carbon loamy sand, 96% for fibres and 89% for particles in sandy loam, and 97% for fibres and 94% for particles in high-clay sandy loam. These were significantly higher than recoveries achieved by DS, particularly for fibres and high-density MPs (p<0.05). To demonstrate the practical application of the HGMS method, it was applied to a farm soil sample, and high-density MP particles were only recovered by HGMS. Furthermore, this study showed that HGMS can recover fibre-aggregate complexes. This improved extraction method will provide better estimates of MP quantities in future studies focused on monitoring the prevalence of MPs in soils

Microbial Biogeography of Six Salt Lakes in Inner Mongolia, China, and a Salt Lake in Argentina ▿ †

We used cultivation-independent methods to investigate the prokaryotic biogeography of the water column in six salt lakes in Inner Mongolia, China, and a salt lake in Argentina. These lakes had different salt compositions and pH values and were at variable geographic distances, on both local and intercontinental scales, which allowed us to explore the microbial community composition within the context of both contemporary environmental conditions and geographic distance. Fourteen 16S rRNA gene clone libraries were constructed, and over 200 16S rRNA gene sequences were obtained. These sequences were used to construct biotic similarity matrices, which were used in combination with environmental similarity matrices and a distance matrix in the Mantel test to discover which factors significantly influenced biotic similarity. We showed that archaeal biogeography was influenced by contemporary environmental factors alone (Na+, CO32−, and HCO3− ion concentrations; pH; and temperature). Bacterial biogeography was influenced both by contemporary environmental factors (Na+, Mg2+, and HCO3− ion concentrations and pH) and by geographic distance