On how the power supply shapes microbial survival

Understanding how environmental factors affect microbial survival is an important open problem in microbial ecology. Patterns of microbial community structure have been characterized across a wide range of different environmental settings, but the mechanisms generating these patterns remain poorly understood. Here, we use mathematical modelling to investigate fundamental connections between chemical power supply to a system and patterns of microbial survival. We reveal a complex set of interdependences between power supply and distributions of survival probability across microbial habitats, in a case without interspecific resource competition. We also find that different properties determining power supply, such as substrate fluxes and Gibbs energies of reactions, affect microbial survival in fundamentally different ways. Moreover, we show how simple connections between power supply and growth can give rise to complex patterns of microbial survival across physicochemical gradients, such as pH gradients. Our findings show the importance of taking energy fluxes into account in order to reveal fundamental connections between microbial survival and environmental conditions, and to obtain a better understanding of microbial population dynamics in natural environments.publishedVersio

Microbial Communities in a Flow-Through Fish Farm for Lumpfish (Cyclopterus lumpus L.) During Healthy Rearing Conditions

Lumpfish can efficiently remove sea lice from Atlantic salmon in net-pens, and production of lumpfish in closed fish farms is a new, fast developing industry in Norway. However, periodic outbreaks of bacterial diseases in the fish farms represent a large problem, both economically and ethically. Therefore it is important to obtain a better understanding of how microbial communities develop in these production facilities. Knowledge on the characteristics of microbial communities associated with healthy fish could also enable detection of changes associated with disease outbreaks at an early stage. In this study we have monitored microbial communities in a fish farm for lumpfish during normal operational conditions with no disease outbreak by using 16S rRNA gene amplicon sequencing. The study involved weekly samplings of water and biofilms from fish tanks, and fish. The results revealed that the microbial communities in fish tank water were different from the intake water. The water and biofilm in fish tanks were highly similar in regards to microbial community members, but with large differences in relative abundances for some taxa. The sampled fish were associated with mostly the same taxa as in tank water and biofilm, but more variation in relative abundances of different taxonomic groups occurred. The microbial communities in the fish farm seemed stable over time, and were dominated by marine bacteria and archaea within Alphaproteobacteria, Epsilonproteobacteria, Flavobacteria, Gammaproteobacteria, Thaumarchaeota, Planctomycetes, Sphingobacteriia, and Verrucomicrobiae (>10% relative abundance). Bacterial genera known to include fish-pathogenic strains were detected in all types of sample materials, but with low relative abundances (<5%). Exceptions were some samples of fish, biofilm and water with high relative abundance of Tenacibaculum (<85.8%) and Moritella (<82%). In addition, some of the eggs had a high relative abundance of Tenacibaculum (<89.5%). Overall, this study shows that a stable microbial community dominated by various genera of non-pathogenic bacteria is associated with a healthy environment for rearing lumpfish. Taxa with pathogenic members were also part of the microbial communities during healthy conditions, but the stable non-pathogenic bacteria may limit their growth and thereby prevent disease outbreaks.publishedVersio

Indigenous Ammonia-Oxidizing Archaea in Oxic Subseafloor Oceanic Crust

Oceanic ridge flank systems represent one of the largest and leastexplored microbial habitats on Earth. Fundamental ecological questions regarding community activity, recruitment, and succession in this environment remain unanswered. Here, we investigated ammonia-oxidizing archaea (AOA) in the sedimentburied basalts on the oxic and young ridge flank at North Pond, a sediment-filled pond on the western flank of the Mid-Atlantic Ridge, and compared them with those in the overlying sediments and bottom seawater. Nitrification in the North Pond basement is thermodynamically favorable and is supported by a reactiontransport model simulating the dynamics of nitrate in the crustal fluids. Nitrification rate is estimated to account for 6% to 7% of oxygen consumption, which is similar to the ratios found in marine oxic sediments, suggesting that aerobic mineralization of organic matter is the major ammonium source for crustal nitrifiers. Using the archaeal 16S rRNA and amoA genes as phylogenetic markers, we show that AOA, composed solely of Nitrosopumilaceae, are the major archaeal dwellers at North Pond. Phylogenetic analysis reveals that the crustal AOA communities are distinct from those in the bottom seawater and the upper oxic sediments but are similar to those in the basal part of the overlying sediment column, suggesting either similar environmental selection or the dispersal of microbes across the sediment-basement interface. Additionally, quantitative abundance data suggest enrichment of the dominant Nitrosopumilaceae clade (Eta clade) in the basement compared to the seawater. This study explored AOA and their activity in the upper oceanic crust, and our results have ecological implications for the biogeochemical cycling of nitrogen in the crustal subsurface

Andromeda's Parachute: Time Delays and Hubble Constant

The gravitational lens system PS J0147+4630 (Andromeda's Parachute) consists of four quasar images ABCD and a lensing galaxy. We obtained $r$-band light curves of ABCD in the 2017$-$2022 period from monitoring with two 2-m class telescopes. Applying state-of-the-art curve shifting algorithms to these light curves led to measurements of time delays between images, and the three independent delays relative to image D are accurate enough to be used in cosmological studies (uncertainty of about 4%): $\Delta t_{\rm{AD}}$ = $-$170.5 $\pm$ 7.0, $\Delta t_{\rm{BD}}$ = $-$170.4 $\pm$ 6.0, and $\Delta t_{\rm{CD}}$ = $-$177.0 $\pm$ 6.5 d, where image D is trailing all the other images. Our finely sampled light curves and some additional fluxes in the years 2010$-$2013 also demonstrated the presence of significant microlensing variations. From the measured delays relative to image D and typical values of the external convergence, recent lens mass models yielded a Hubble constant that is in clear disagreement with currently accepted values around 70 km s$^{-1}$ Mpc$^{-1}$. We discuss how to account for a standard value of the Hubble constant without invoking the presence of an extraordinary high external convergence.Comment: 10 pages, 4 figures, 4 tables (full version of Table 2 is only available in electronic form). Accepted for publication in ApJ. arXiv admin note: substantial text overlap with arXiv:2206.0926

The Sunburst Arc: Direct Lyman {\alpha} escape observed in the brightest known lensed galaxy

We present rest-frame ultraviolet and optical spectroscopy of the brightest lensed galaxy yet discovered, at redshift z = 2.4. This source reveals a characteristic, triple-peaked Lyman {\alpha} profile which has been predicted by various theoretical works but to our knowledge has not been unambiguously observed previously. The feature is well fit by a superposition of two components: a double-peak profile emerging from substantial radiative transfer, and a narrow, central component resulting from directly escaping Lyman {\alpha} photons; but is poorly fit by either component alone. We demonstrate that the feature is unlikely to contain contamination from nearby sources, and that the central peak is unaffected by radiative transfer effects apart from very slight absorption. The feature is detected at signal-to-noise ratios exceeding 80 per pixel at line center, and bears strong resemblance to synthetic profiles predicted by numerical models.Comment: Accepted for publication in Astronomy & Astrophysics. 4 pages, 5 figure

The Microbiome and Occurrence of Methanotrophy in Carnivorous Sponges

As shown by recent studies, filter-feeding sponges are known to host a wide variety of microorganisms. However, the microbial community of the non-filtering carnivorous sponges (Porifera, Cladorhizidae) has been the subject of less scrutiny. Here, we present the results from a comparative study of the methanotrophic carnivorous sponge Cladorhiza methanophila from a mud volcano-rich area at the Barbados Accretionary Prism, and five carnivorous species from the Jan Mayen Vent Field (JMVF) at the Arctic Mid-Ocean Ridge. Results from 16S rRNA microbiome data indicate the presence of a diverse assemblage of associated microorganisms in carnivorous sponges mainly from the Gamma- and Alphaproteobacteria, Flavobacteriaceae, and Thaumarchaeota. While the abundance of particular groups varied throughout the dataset, we found interesting similarities to previous microbiome results from non-carnivorous deep sea sponges, suggesting that the carnivorous sponges share characteristics of a previously hypothesized putative deep-sea sponge microbial community. Chemolithoautotrophic symbiosis was confirmed for C. methanophila through a microbial community with a high abundance of Methylococcales and very light isotopic δ13C and δ15N ratios (-60 to -66‰/3.5 to 5.2‰) compared to the other cladorhizid species (-22 to -24‰/8.5 to 10.5‰). We provide evidence for the presence of putative sulfur-oxidizing Gammaproteobacteria in the arctic cladorhizids; however, δ13C and δ15N signatures did not provide evidence for significant chemoautotrophic symbiosis in this case, and the slightly higher abundance of cladorhizids at the JMVF site compared to the nearby deep sea likely stem from an increased abundance of prey rather than a more direct vent association. The phylogenetic position of C. methanophila in relation to other carnivorous sponges was established using a three-gene phylogenetic analysis, and it was found to be closely related to other non-methanotrophic Cladorhiza species with a similar morphology included in the dataset, suggesting a recent origin for methanotrophy in this species. C. methanophila remains the only known carnivorous sponge with a strong, chemolithoautotrophic symbiont association, and methanotrophic symbiosis does not seem to be a widespread property within the Cladorhizidae.publishedVersio

Fine-Scale Community Structure Analysis of ANME in Nyegga Sediments with High and Low Methane Flux

To obtain knowledge on how regional variations in methane seepage rates influence the stratification, abundance, and diversity of anaerobic methanotrophs (ANME), we analyzed the vertical microbial stratification in a gravity core from a methane micro-seeping area at Nyegga by using 454-pyrosequencing of 16S rRNA gene tagged amplicons and quantitative PCR. These data were compared with previously obtained data from the more active G11 pockmark, characterized by higher methane flux. A down core stratification and high relative abundance of ANME were observed in both cores, with transition from an ANME-2a/b dominated community in low-sulfide and low methane horizons to ANME-1 dominance in horizons near the sulfate-methane transition zone. The stratification was over a wider spatial region and at greater depth in the core with lower methane flux, and the total 16S rRNA copy numbers were two orders of magnitude lower than in the sediments at G11 pockmark. A fine-scale view into the ANME communities at each location was achieved through operational taxonomical units (OTU) clustering of ANME-affiliated sequences. The majority of ANME-1 sequences from both sampling sites clustered within one OTU, while ANME-2a/b sequences were represented in unique OTUs. We suggest that free-living ANME-1 is the most abundant taxon in Nyegga cold seeps, and also the main consumer of methane. The observation of specific ANME-2a/b OTUs at each location could reflect that organisms within this clade are adapted to different geochemical settings, perhaps due to differences in methane affinity. Given that the ANME-2a/b population could be sustained in less active seepage areas, this subgroup could be potential seed populations in newly developed methane-enriched environments

Gravitational lensing reveals ionizing ultraviolet photons escaping from a distant galaxy

During the epoch of reionisation, neutral gas in the early Universe was ionized by hard ultraviolet radiation emitted by young stars in the first galaxies. To do so, ionizing ultraviolet photons must escape from the host galaxy. We present Hubble Space Telescope observations of the gravitationally lensed galaxy PSZ1-ARC G311.6602-18.4624, revealing bright, multiply-imaged ionizing photon escape from a compact star-forming region through a narrow channel in an optically thick gas. The gravitational lensing magnification shows how ionizing photons escape this galaxy, contributing to the re-ionization of the Universe. The multiple sight lines to the source probe absorption by intergalactic neutral hydrogen on scales of no more than a few hundred, perhaps even less than ten, parsec.Comment: 17 pages, 9 figures. Published in Scienc

Exploring codon adjustment strategies towards Escherichia coli-based production of viral proteins encoded by HTH1, a novel prophage of the marine bacterium Hypnocyclicus thermotrophus

Marine viral sequence space is immense and presents a promising resource for the discovery of new enzymes interesting for research and biotechnology. However, bottlenecks in the functional annotation of viral genes and soluble heterologous production of proteins hinder access to downstream characterization, subsequently impeding the discovery process. While commonly utilized for the heterologous expression of prokaryotic genes, codon adjustment approaches have not been fully explored for viral genes. Herein, the sequence-based identification of a putative prophage is reported from within the genome of Hypnocyclicus thermotrophus, a Gram-negative, moderately thermophilic bacterium isolated from the Seven Sisters hydrothermal vent field. A prophage-associated gene cluster, consisting of 46 protein coding genes, was identified and given the proposed name Hypnocyclicus thermotrophus phage H1 (HTH1). HTH1 was taxonomically assigned to the viral family Siphoviridae, by lowest common ancestor analysis of its genome and phylogeny analyses based on proteins predicted as holin and DNA polymerase. The gene neighbourhood around the HTH1 lytic cassette was found most similar to viruses infecting Gram-positive bacteria. In the HTH1 lytic cassette, an N-acetylmuramoyl-L-alanine amidase (Amidase_2) with a peptidoglycan binding motif (LysM) was identified. A total of nine genes coding for enzymes putatively related to lysis, nucleic acid modification and of unknown function were subjected to heterologous expression in Escherichia coli. Codon optimization and codon harmonization approaches were applied in parallel to compare their effects on produced proteins. Comparison of protein yields and thermostability demonstrated that codon optimization yielded higher levels of soluble protein, but codon harmonization led to proteins with higher thermostability, implying a higher folding quality. Altogether, our study suggests that both codon optimization and codon harmonization are valuable approaches for successful heterologous expression of viral genes in E. coli, but codon harmonization may be preferable in obtaining recombinant viral proteins of higher folding quality.publishedVersio

Hubble Constant Measurement from Three Large-separation Quasars Strongly Lensed by Galaxy Clusters

Tension between cosmic microwave background–based and distance ladder–based determinations of the Hubble constant H 0 motivates the pursuit of independent methods that are not subject to the same systematic effects. A promising alternative, proposed by Refsdal in 1964, relies on the inverse scaling of H 0 with the delay between the arrival times of at least two images of a strongly lensed variable source such as a quasar. To date, Refsdal’s method has mostly been applied to quasars lensed by individual galaxies rather than by galaxy clusters. Using the three quasars strongly lensed by galaxy clusters (SDSS J1004+4112, SDSS J1029+2623, and SDSS J2222+2745) that have both multiband Hubble Space Telescope data and published time delay measurements, we derive H 0, accounting for the systematic and statistical sources of uncertainty. While a single time delay measurement does not yield a well-constrained H 0 value, analyzing the systems together tightens the constraint. Combining the six time delays measured in the three cluster-lensed quasars gives H 0 = 74.1 ± 8.0 km s−1 Mpc−1. To reach 1% uncertainty in H 0, we estimate that a sample size of order of 620 time delay measurements of similar quality as those from SDSS J1004+4112, SDSS J1029+2623, and SDSS J2222+2745 would be needed. Improving the lens modeling uncertainties by a factor of two and a half may reduce the needed sample size to 100 time delays, potentially reachable in the next decade