Biology subjects

Hansen, L. H.

Publications and source records attributed to Hansen, L. H..

At least 37 records · Page 2Linked to original sources

bioRxiv2021

Analyses of the complete genome sequence of 2,6-dichlorobenzamide (BAM) degrader Aminobacter sp. MSH1 suggests a polyploid chromosome, phylogenetic reassignment, and functions of (un)stable plasmids.

Aminobacter sp. MSH1 (CIP 110285) can use the pesticide dichlobenil and its transformation product, the recalcitrant groundwater micropollutant, 2,6-dichlorobenzamide (BAM) as sole source of carbon, nitrogen, and energy. The concentration of BAM in groundwater often exceeds the threshold limit for drinking water, resulting in the use of additional treatment in drinking water treatment plants (DWTPs) or closure of the affected abstraction wells. Biological treatment with MSH1 is considered a potential sustainable alternative to remediate BAM-contamination in drinking water production. Combining Illumina and Nanopore sequencing, we here present the complete genome of MSH1, which was determined independently in two different laboratories. Unexpectedly, divergences were observed between the two genomes, i.e. one of them lacked four plasmids compared to the other. Besides the circular chromosome and the two previously described plasmids involved in BAM catabolism pBAM1 (41 kb) and pBAM2 (54 kb), we observe that the genome of MSH1 contains two megaplasmids pUSP1 (367 kb) and pUSP2 (366 kb) and three smaller plasmids pUSP3 (97 kb), pUSP4 (64 kb), and pUSP5 (32 kb). The MSH1 substrain from KU Leuven showed a reduced genome lacking plasmids pUSP2 and the three smaller plasmids and was designated substrain MK1, whereas the variant with all plasmids was designated as substrain DK1. Results of a plasmid stability experiment, indicate that strain MSH1 may have a polyploid chromosome when growing in R2B medium with more chromosomes than plasmids per cell. Based on phylogenetic analyses, strain MSH1 is reassigned as Aminobacter niigataensis MSH1. ImportanceThe complete genomes of the two MSH1 substrains, DK1 and MK1, provide further insight into this already well-studied organism with bioremediation potential. The varying plasmid contents in the two substrains suggest that some of the plasmids are unstable, although this is not supported by the herein described plasmid stability experiment. Instead, results suggest that MSH1 is polyploid with respect to its chromosome, at least under some growth conditions. As the essential BAM-degradation genes are found on some of these plasmids, stable inheritance is essential for continuous removal of BAM. Finally, Aminobacter sp. MSH1 is reassigned as Aminobacter niigataensis MSH1, based on phylogenetic evidence.

microbiology↗

bioRxiv2021

Mobilization of antibiotic resistance genes differ by resistance mechanism

The degree to which antibiotic resistance genes (ARGs) are mobilized by insertion sequence (IS) elements, plasmids, and integrons has a strong association with their likelihood to function as resistance determinants. This stems from genetic decontextualization where strong promoters often present in IS elements and integrons and the copy number effect of plasmids contribute to high expression of accessory genes. Here, we screen all complete bacterial RefSeq genomes for ARGs. The genetic contexts of detected ARGs are investigated for IS elements, integrons, plasmids, and phylogenetic dispersion. The ARG-MOB scale is proposed which indicates how mobilized detected ARGs are in bacterial genomes. Antibiotic efflux genes are rarely mobilized and it is concluded that these are often housekeeping genes that are not decontextualized to confer resistance through overexpression. Even 80% of {beta}-lactamases have never, or very rarely, been mobilized in the 15,790 studied genomes. However, some ARGs are indeed mobilized and co-occur with IS elements, plasmids, and integrons. These results have consequences for the design and interpretation of studies screening for resistance determinants, as mobilized ARGs pose a more concrete risk to human health, especially under heterologous expression, than groups of ARGs that have only been shown to confer resistance in cloning experiments.

microbiology↗

bioRxiv2020

Potential Rhodopsin and Bacteriochlorophyll-Based Dual Phototrophy in a High Arctic Glacier

Conserving additional energy from sunlight through bacteriochlorophyll (BChl)-based reaction center or proton-pumping rhodopsin is a highly successful life strategy in environmental bacteria. Rhodopsin and BChl based systems display contrasting characteristics in the size of coding operon, cost of biosynthesis, ease of expression control, and efficiency of energy production. This raises an intriguing question of whether a single bacterium has evolved the ability to perform these two types of phototrophy complementarily according to energy needs and environmental conditions. Here we report four Tardiphaga sp. strains (Alphaproteobacteria) of monophyletic origin isolated from a high Arctic glacier in northeast Greenland (81.566{degrees} N, 16.363{degrees} W) that are at different evolutionary stages concerning phototrophy. Their >99.8% identical genomes contain footprints of horizontal operon transfers (HOT) of the complete gene clusters encoding BChl and xanthorhodopsin (XR)-based dual phototrophy. Two strains only possess a complete xanthorhodopsin (XR) operon, while the other two strains have both a photosynthesis gene cluster (PGC) and an XR operon in their genomes. All XR operons are heavily surrounded by mobile genetic elements and located close to a tRNA gene, strongly signaling that a HOT event of XR operon has occurred recently. Mining public genome databases and our High Arctic glacial and soil metagenomes revealed that phylogenetically diverse bacteria have the metabolic potential of performing BChl and rhodopsin-based dual phototrophy. Our data provide new insights on how bacteria cope with the harsh and energy-deficient environments in surface glaciers, possibly by maximizing the capability of exploiting solar energy. ImportanceOver billions of years of evolution, bacteria capable of light-driven energy production have occupied every corner of surface Earth where solar irradiation can reach. Only two general biological systems have evolved in bacteria to be capable of net energy conservation via light-harvesting: one is based on the pigment of (bacterio-)chlorophyll and the other based on light-sensing retinal molecules. There is emerging genomic evidence that these two rather different systems can co-exist in a single bacterium to take advantage of their contrasting characteristics in the number of genes involved, biosynthesis cost, ease of expression control and efficiency of energy production, and thus enhance the capability of exploiting solar energy. Our data provide the first clear-cut evidence that such dual phototrophy potentially exist in glacial bacteria. Further public genome mining suggests this understudied dual phototrophic mechanism is possibly more common than our data alone suggested. Sequence data availabilityGenomes, metagenomes and raw reads were deposited into GenBank under Bioprojects PRJNA548505 and PRJNA552582.

microbiology↗

bioRxiv2020

Microbial map of the world's vineyards:Applying the concept of microbial terroir on a global scale

The specific microbial biodiversity linked to a particular vineyard location is reported to be a crucial aspect, in conjunction with edaphic, climatic and human factors, in the concept of wine terroir. These biogeographical patterns are known as microbial terroirs. This study applied an HTS amplicon library approach in order to conduct a global survey of vineyards soil microbial communities. In all, soil samples from 200 vineyards on four continents were analysed in an attempt to establish the basis for the development of a vineyard soil microbiome map to represent microbial wine terroirs on a global scale. This study established links between vineyard locations and microbial biodiversity on different scales: between continents and countries, and between different wine regions within the same country. Geography had a strong effect on the composition of microbial communities on a global scale, which was also maintained on a country scale. Furthermore, a predictive model was developed, based on random forest analyses, to discriminate between microbial patterns in order to identify the geographical source of the samples with reasonable precision. Finally this study is the first to describe the microbial community of new and northern wine-producing regions, such as Denmark, that could be of great interest for viticulture adaptation in a context of climate change.

microbiology↗

bioRxiv2020

Bioaugmented sand filter columns provide stable removal of pesticide residue from membrane retentate

Drinking water resources, such as groundwater, are threatened by pollution. The pesticide metabolite 2,6-dichlorobenzamide (BAM) is one of the compounds frequently found in groundwater. Studies have attempted to add specific BAM-degrading bacteria to sand-filters at drinking water treatment facilities. This biotechnology has shown great potential in removing BAM from contaminated water. However, the degradation potential was formerly lost after approximately 2-3 weeks due to a decrease of the degrader population over time. The aim of the present study was to overcome the constraints leading to loss of degraders from inoculated filters. Our approach was threefold: 1) Development of a novel inoculation strategy, 2) lowering the flowrate to reduce washout of cells, and 3) increasing the concentration of nutrients hereunder the pollutant in a smaller inlet water stream. The two latter were achieved via modifications of the inlet water by applying membrane treatment which, besides producing an ultra-pure water fraction, produced a residual water stream with nutrients including BAM concentrated in an approximately 10-fold reduced volume. This was done to alleviate starvation of degrader bacteria in the otherwise oligotrophic sand-filters and to enable a decreased flowrate. By this approach, we achieved 100% BAM removal over a period of 40 days in sand-filter columns inoculated with the BAM-degrader Aminobacter sp. MSH1. Molecular targeting of the degrader strain showed that the population of degrader bacteria persisted at high numbers throughout the sand-filter columns and over the entire timespan of the experiment. 16S rRNA gene amplicon sequencing confirmed that MSH1 dominated the bacterial communities. IMPORTANCEMany countries rely partly or solely on groundwater as the source of drinking water. Here groundwater contamination by pesticide residues poses a serious threat to the production of high quality drinking water. Since scarcity of clean groundwater may occur in progressively larger areas both locally and globally, the need for efficient purification technologies is growing. This study shows that a novel system combining membrane treatment and bioaugmented sand-filters can efficiently remove pesticide residues in laboratory columns when applying specific inoculation and flow conditions. Once upscaled, this system can be used directly for pump-and-treat of contaminated groundwater wells or at drinking water treatment plants.

microbiology↗

bioRxiv2020

A New High-throughput Screening (HiTS) Method for Phages - Enabling Crude Isolation and Fast Identification of Diverse Phages with Therapeutic Potential

Bacteriophage therapy and application of phages as biocontrol in plant production and food processing, all necessitates acquisition of suitable phages. Depending on purpose, the selection criteria of phage characteristics include lifestyle (lytic/lysogenic), host range, physical stability and absence of unwanted genetic traits such as integrases, antibiotic resistance or bacterial virulence factors. The exclusivity of antibiotic resistant clinical infections and possible development of phage-resistance instigates a need to continually build sizeable phage libraries and also be able to rapidly isolate and characterise novel phages of specified bacterial hosts. Current methods for phage isolation are both laborious and time consuming, suitable only for the isolation of a limited number of phages. Thus, we developed the High-Throughput Screening (HITS) method for phages for fast isolation and identification of potentially hundreds of distinct phages against single hosts. This scalable method enables screening of hundreds of samples, in multiple simultaneous setups with varying parameters increasing the likelihood of isolating multiple distinct phages specific for the given conditions. The efficiency of the method is emphasised by our screening of 200 environmental samples, resulting in the identification of an abundance of unique phage species lytic to Escherichia coli, Salmonella Enterica, Enterococcus faecalis and Pseudomonas aeruginosa.

microbiology↗

bioRxiv2020

Genomic characterization of three novel Pseudomonas phages within the subfamily of Autographivirinae isolated from organic waste

Three phages targeting Pseudomonas syringae GAW0113 have been isolated from organic waste samples: Pseudomonas phage Bertil, Misse and Strit. The phages have double-stranded DNA genomes ranging from 41342 to 41374 bp in size comprising 50 to 51 open reading frames. The three phages genomes are highly similar and genomic comparison analyses shows that they all belong to the Autographivirinae subfamily of the family Podoviridae. The phages are however only distantly related to other members of this family, and have limited gene synteny with type-phages of other genera within Autographivirinae, suggesting that the newly isolated phages could represent a new genus.

microbiology↗

bioRxiv2020

Exploring the remarkable diversity of Escherichia coli Phages in the Danish Wastewater Environment, Including 91 Novel Phage Species

Phages drive bacterial diversity - profoundly influencing diverse microbial communities, from microbiomes to the drivers of global biogeochemical cycling. The vast genomic diversity of phages is gradually being uncovered as >8000 phage genomes have now been sequenced. Aiming to broaden our understanding of Escherichia coli (MG1655, K-12) phages, we screened 188 Danish wastewater samples (0.5 ml) and identified 136 phages of which 104 are unique phage species and 91 represent novel species, including several novel lineages. These phages are estimated to represent roughly a third of the true diversity of Escherichia phages in Danish wastewater. The novel phages are remarkably diverse and represent four different families Myoviridae, Siphoviridae, Podoviridae and Microviridae. They group into 14 distinct clusters and nine singletons without any substantial similarity to other phages in the dataset. Their genomes vary drastically in length from merely 5 342 bp to 170 817 kb, with an impressive span of GC contents ranging from 35.3% to 60.0%. Hence, even for a model host bacterium, in the go-to source for phages, substantial diversity remains to be uncovered. These results expand and underlines the range of Escherichia phage diversity and demonstrate how far we are from fully disclosing phage diversity and ecology.

microbiology↗

bioRxiv2020

Isolation and complete genome sequencing of Pectobacterium phage Jarilo, representing a novel genus of bacteriophages within the subfamily Autographivirinae

Pectobacterium carotovorum is the causative agent of bacterial soft rot on various plant species. The use of phages for plant disease control have gained increased awareness over the past years. We here describe the isolation and characterization of Pectobacterium phage Jarilo, representing a novel genus of bacteriophages within the subfamily Autographivirinae. Jarilo possesses a double-stranded DNA genome of 40557 bp with a G+C% content of 50.08% and 50 predicted open reading frames (ORFs). Gene synteny and products seem to be somewhat conserved between Pectobacterium phage Jarilo and Enterobacteria phage T7, but limited nucleotide similarity is found between Jarilo and other phages within the subfamily Autographivirinae. We propose Pectobacterium phage Jarilo as the first member of a new genus of bacteriophages within the subfamily Autographivirinae.

microbiology↗

bioRxiv2019

Physical fitness in community dwelling older adults is linked to dietary intake, gut microbiota and metabolomic signatures

When humans age, changes in body composition arise along with lifestyle-associated disorders influencing fitness and physical decline. Here we provide a comprehensive view of dietary intake, physical activity, gut microbiota (GM) and host metabolome in relation to physical fitness of 207 community dwelling subjects aged +65 years. Stratification on anthropometric/body-composition/physical-performance measurements (ABPm) variables identified two phenotypes (high/low-fitness) clearly linked to dietary intake, physical activity, GM and host metabolome patterns. Strikingly, despite a higher energy intake high-fitness subjects were characterized by leaner bodies and lower fasting proinsulin-C-peptide/blood glucose levels in a mechanism likely driven by higher dietary-fiber intake, physical activity and increased abundance of Bifidobacteriales and Clostridiales species in GM and associated metabolites (i.e. enterolactone). These factors explained 50.1% of the individual variation in physical fitness. We propose that targeting dietary strategies for modulation of GM and host metabolome interactions may allow establishing therapeutic approaches to delay and possibly revert comorbidities of aging.

cell biology↗

bioRxiv2019

Faecal virome transplantation decrease symptoms of type-2-diabetes and obesity in a murine model

ObjectiveDevelopment of obesity and type-2-diabetes (T2D) are associated with gut microbiota (GM) changes. The gut viral community is predominated by bacteriophages (phages), which are viruses that attack bacteria in a host-specific manner. As a proof-of-concept we demonstrate the efficacy of faecal virome transplantation (FVT) from lean donors for shifting the phenotype of obese mice into closer resemblance of lean mice.\n\nDesignThe FVT consisted of viromes extracted from the caecal content of mice fed a low-fat (LF) diet for fourteen weeks. Male C57BL/6NTac mice were divided into five groups: LF (as control), high-fat diet (HF), HF+Ampicillin (Amp), HF+Amp+FVT and HF+FVT. At week six and seven of the study the HF+FVT and HF+Amp+FVT mice were treated with FVT by oral gavage. The Amp groups were treated with ampicillin 24 h prior to first FVT treatment.\n\nResultsSix weeks after first FVT the HF+FVT mice showed a significant decrease in weight gain compared to the HF group. Further, glucose tolerance was comparable between the lean LF and HF+FVT mice, while the other HF groups all had impaired glucose tolerance. These observations were supported by significant shifts in GM composition, blood plasma metabolome, and expression levels of genes involved in obesity and T2D development.\n\nConclusionsTransfer of gut viral communities from mice with a lean phenotype into those with an obese phenotype reduce weight gain and normalise blood glucose parameters relative to lean mice. We hypothesise that this effect is mediated via FVT-induced GM changes.\n\nSignificance of this studyWhat is already known about this subject?\n\nO_LIObesity and type-2-diabetes (T2D) are associated with gut microbiota (GM) dysbiosis.\nC_LIO_LIFaecal microbiota transplant from lean donors has previously shown potential in treating obesity and T2D.\nC_LIO_LIPatients suffering from recurrent Clostridium difficile infections (rCDI) have been cured with sterile filtered donor faeces (containing enteric viruses and no bacteria), here defined as faecal virome transplantation (FVT).\nC_LI\n\nWhat are the new findings?\n\nO_LIFVT from lean donors lead to decreased weight gain and normalised blood sugar tolerance in a diet-induced obesity (DIO) mouse model.\nC_LIO_LIFVT significantly changed the bacterial and viral GM component, as well as the plasma metabolome and the expression profiles of obesity and T2D associated genes.\nC_LIO_LIInitial treatment with ampicillin prior FVT seems to counteract the beneficial effects associated with FVT.\nC_LI\n\nHow might it impact on clinical practice in the foreseeable future?\n\nO_LIWe here show a proof-of-concept, providing a solid base for designing a clinical study of FVT targeting obesity and T2D in humans. This is further augmented by the increased safety related to FVT, since bacteria and other microorganisms are removed from the donor faeces, and therefore minimises the risk of disease transmission.\nC_LIO_LIThese findings highlight the potential application of FVT treatment of various diseases related to GM dysbiosis and further support the vital role of the viral community in maintaining and shaping the GM.\nC_LI

microbiology↗

bioRxiv2019

Loss of Bacterial Cell Pole Stabilization in Caulobacter crescentus Sensitizes to Outer Membrane Stress and Peptidoglycan-Directed Antibiotics

Rod-shaped bacteria frequently localise proteins to one or both cell poles in order to regulate processes such as chromosome replication or polar organelle development. However, the role of such polar factors in responses to extracellular stimuli has been generally unexplored. We employed chemical-genetic screening to probe the interaction between one such factor from Caulobacter crescentus, TipN, and extracellular stress and found that TipN is required for normal tolerance of cell envelope-directed antibiotics, including vancomycin that does not normally inhibit growth of Gram-negative bacteria. Forward genetic screening for suppressors of vancomycin sensitivity in the absence of TipN revealed the TonB-dependent receptor ChvT as the mediator of vancomycin tolerance. Loss of ChvT improved resistance to vancomycin and cefixime in the otherwise sensitive {Delta}tipN strain. The activity of the two-component system regulating ChvT (ChvIG) was increased in {Delta}tipN cells relative to wild type under some, but not all, cell wall stress conditions that this strain was sensitised to, in particular cefixime and detergent exposure. Together, these results indicate that the ChvIG two-component system has been co-opted as a sensor of cell wall stress and that TipN can influence cell envelope stability and ChvIG-mediated signaling in addition to its roles in intracellular development.\n\nAuthor summaryMaintenance of an intact cell envelope is essential for free-living bacteria to survive harsh conditions they may encounter in their environment. In the case of rod-shaped bacteria, the poles of the cell are potential weak points in the cell envelope due to the high curvature of the layers and the need to break and re-form parts of the cell envelope at the division plane in order to form new poles as the cells replicate and divide. We have found that TipN, a factor required for correct division and cell pole development in the rod-shaped bacterium, Caulobacter crescentus, is also needed for maintaining normal levels of resistance to cell wall-targeting antibiotics such as vancomycin and cefixime, which interfere with peptidoglycan synthesis. We also identified an outer membrane receptor, ChvT, that was responsible for allowing vancomycin access to the cells and found that the two-component system that negatively regulates ChvT production was activated by various kinds of cell wall stress. Presence or absence of TipN influenced how active this system was in the presence of cefixime or of the membrane-disrupting detergent sodium deoxycholate. Since TipN is normally located at the poles of the cell and at the division plane just before cells complete division, our results suggest that it is involved in stabilisation of these weak points of the cell envelope as well as its other roles inside the cell.

microbiology↗

bioRxiv2019

A novel and direct mobilome approach improves the detection of larger-sized circular elements across kingdoms

Mobile genetic elements (MGEs) are instrumental in natural prokaryotic genome editing, permitting genome plasticity and allowing microbes to accumulate immense genetic diversity. MGEs include DNA elements such as plasmids, transposons and Insertion Sequences (IS-elements), as well as bacteriophages (phages), and they serve as a vast communal gene pool. These mobile DNA elements represent a human health risk as they can add new traits, such as antibiotic resistance or virulence, to a bacterial strain. Sequencing libraries targeting circular MGEs, referred to as mobilomes, allows the expansion of our current understanding of the mechanisms behind the mobility, prevalence and content of these elements. However, metamobilomes from bacterial communities are not studied to the same extent as metagenomics, partly because of methodological biases arising from multiple displacement amplification (MDA), often used in previous metamobilome publications. In this study, we show that MDA is detrimental to the detection of larger-sized plasmids if small plasmids are present by comparing the abundances of reads mapping to plasmids in a wastewater sample spiked with a mock community of selected plasmids with and without MDA. Furthermore, we show that it is possible to produce samples consisting almost exclusively of circular MGEs and obtain a catalog of larger, complete, circular MGEs from complex samples without the use of MDA.\n\nImportanceMobile genetic elements (MGEs) can transport genetic information between genomes in different bacterial species, adding new traits, potentially generating dangerous multidrug-resistant pathogens. In fact, plasmids and circular MGEs can encode bacterial genetic specializations such as virulence, resistance to metals, antimicrobial compounds, and bacteriophages, as well as the degradation of xenobiotics. For this reason, circular MGEs are crucial to investigate, but they are often missed in metagenomics and ecological studies. In this study, we present, for the first time, an improved method, which reduces the bias towards small MGEs and we demonstrate that this method can unveil larger, complete circular MGEs from complex samples without the use of multiple displacement amplification. This method may result in the detection of larger-sized plasmids that have hitherto remained unnoticed and therefore has the potential to reveal novel accessory genes, acting as possible targets in the development of preventive strategies directed at pathogens.

microbiology↗

bioRxiv2019

Mouse vendor influence on the bacterial and viral gut composition exceeds the effect of diet

Often physiological studiess using mice from one vendor show different outcome when being reproduced using mice from another vendor. These divergent phenotypes between similar mouse strains from different vendors have been assigned to differences in the gut microbiome. During recent years, evidence has mounted that the gut viral community plays a key role in shaping the gut microbiome and may thus also influence mouse phenotype. However, to date inter-vendor variation in the murine gut virome has not been studied. Using a metavirome approach, combined with 16S rRNA gene sequencing, we here compare the composition of the viral and bacterial gut community of C57BL/6N mice from three different vendors exposed to either a chow-based low-fat diet or high-fat diet. Interestingly, both the bacterial and the viral component of the gut community differed significantly between vendors. The different diets also strongly influenced both the viral and bacterial gut community, but surprisingly the effect of vendor exceeded the effect of diet. In conclusion, the vendor effect is substantial on not only the gut bacterial community, but also strongly influences viral community composition. Given the effect of GM on mice phenotype this is essential to consider, for increasing reproducibility of mouse studies.

microbiology↗

bioRxiv2019

Seasonal microbial dynamics on grapevine leaves under biocontrol and copper fungicide treatments

Winemakers have long used copper as a fungicide on grapevine. However, the potential of copper to accumulate on soil and affect the biota poses a challenge to achieving sustainable agriculture. One recently developed option is the use of biocontrol agents to replace or complement traditional methods. In the present study, a field experiment was conducted in South Africa in which the leaves in two blocks of a vineyard were periodically treated with either copper sulphate or sprayed with Lactobacillus plantarum MW-1 as a biocontrol agent. This study evaluated the impact of the two treatments on the bacterial and fungal communities as they changed during the growing season. To do this, NGS was combined with quantitative strain-specific and community qPCRs. The results revealed the progression of the microbial communities throughout the season and how the different treatments affected the microbiota. Bacteria appeared to be relatively stable at the different time points, with the only taxa that systematically changed between treatments being Lactobacillaceae, which included reads from the biocontrol agent. Cells of Lactobacillus plantarum MW-1 were only detected on treated leaves using strain-specific qPCR, with its amount spanning from 103to 105cells/leaves. Conversely the fungal community was largely shaped by a succession of different dominant taxa over the months. Between treatments, only a few fungal taxa appeared to change significantly and the number of ITS copies was also comparable. In this regards, the two treatments seemed to affect the microbial community similarly, revealing the potential of this biocontrol strain as a promising alternative among sustainable fungicide treatments, although further investigation is required.

microbiology↗

bioRxiv2018

The whole genome sequence and mRNA transcriptome of the tropical cyclopoid copepod Apocyclops royi

Copepoda is one of the most ecologically important animal groups on Earth, yet very few genetic resources are available for this Subclass. Here, we present the first whole genome sequence (WGS, acc. UYDY01) and the first mRNA transcriptome assembly (TSA, Acc. GHAJ01) for the tropical cyclopoid copepod species Apocyclops royi. Until now, only the 18S small subunit of ribosomal RNA gene and the COI gene has been available from A. royi, and only one other cyclopoid copepod had WGS resources available. Overall, the provided resources are the 7th copepod species to have WGS available and the 19th copepod species with TSA information available. We analyze the length and GC content of the provided WGS scaffolds as well as the coverage and gene content of both the WGS and the TSA assembly. Finally, we place the resources within the copepod order Cyclopoida as a member of the Apocyclops genus. We estimate the total genome size of A. royi to 450 Mb, with 181 Mb assembled nonrepetitive, 76 Mb assembled repeats and 193Mb unassembled sequence. The TSA assembly consists of 29,737 genes and an additional 45,756 isoforms. In the WGS and TSA assemblies, >80% and >95% of core genes can be found, though many in fragmented versions. The provided resources will allow researchers to conduct physiological experiments on A. royi, and also increase the possibilities for copepod gene set analysis, as it adds substantially to the copepod datasets available.

genomics↗

bioRxiv2018

Culturomics of Aerobic Anoxygenic Phototrophic Bacteria in Wheat Phyllosphere Revealed a Divergent Evolutionary Pattern of Photosynthesis Genes in Methylobacterium spp.

The phyllosphere is a habitat to a variety of viruses, bacteria, fungi and other microorganisms, which play a fundamental role in maintaining the health of plants and mediating the interaction between plants and ambient environments. A recent addition to this catalogue of microbial diversity was the aerobic anoxygenic phototrophs (AAPs), a group of widespread bacteria that absorb light through bacteriochlorophyll (BChl a) to produce energy without fixing carbon or producing molecular oxygen. However, culture representatives of AAPs from phyllosphere and their genome information are lacking, limiting our capability to assess their potential ecological roles in this unique niche. In this study, we investigated the presence of AAPs in the phyllosphere of a winter wheat (Triticum aestivum L.) in Denmark by employing bacterial colony based infrared imaging and MALDI-TOF mass spectrometry (MS) techniques. A total of ~4480 colonies were screened for the presence of cellular BChl a, resulting in 129 AAP isolates that were further clustered into 25 groups based on MALDI-TOF MS profiling, representatives of which were sequenced using the Illumina NextSeq and Oxford Nanopore MinION platforms. Twenty draft and five complete genomes of AAPs were assembled belonging in Methylobacterium, Rhizobium, Roseomonas and a novel strain in Methylocystaceae. We observed a diverging pattern in the evolutionary rates of photosynthesis genes among the highly homogenous AAP strains of Methylobacterium (Alphaproteobacteria), highlighting an ongoing genomic innovation at the gene cluster level.

microbiology↗

bioRxiv2018

The Genome of BAM-degrading Aminobacter sp. MSH1 with Several Low Copy Plasmids

As one of the only described degraders of the recalcitrant metabolite 2,6-dichlorobenzamide (BAM) of the pesticide dichlobenil, Aminobacter sp. MSH1 has been intensively studied for its characteristics with regards to physiology and its use in bioremediation. Two plasmid sequences from strain MSH1 have previously been published, while the remaining genome sequence has been left uninvestigated. We here present the complete genome sequence of this important strain, which consists of a chromosome, two megaplasmids and five smaller plasmids. Intriguingly, the plasmid copy numbers are mostly below one per bacterial chromosome, indicating that plasmids in strain MSH1 are under very unstable conservation. The results of this report improve our understanding of the genomic dynamics of Aminobacter sp. MSH1.

microbiology↗