Polar front associated variation in prokaryotic community structure in Arctic shelf seafloor

Published version. Also available at http://dx.doi.org/10.3389/fmicb.2015.00017Spatial variations in composition of marine microbial communities and its causes have largely been disclosed in studies comprising rather large environmental and spatial differences. In the present study, we explored if a moderate but temporally permanent climatic division within a contiguous arctic shelf seafloor was traceable in the diversity patterns of its bacterial and archaeal communities. Soft bottom sediment samples were collected at 10 geographical locations, spanning spatial distances of up to 640 km, transecting the oceanic polar front in the Barents Sea. The northern sampling sites were generally colder, less saline, shallower, and showed higher concentrations of freshly sedimented phytopigments compared to the southern study locations. Sampling sites depicted low variation in relative abundances of taxa at class level, with persistent numerical dominance by lineages of Gamma- and Deltaproteobacteria (57–66% of bacterial sequence reads). The Archaea, which constituted 0.7–1.8% of 16S rRNA gene copy numbers in the sediment, were overwhelmingly (85.8%) affiliated with the Thaumarchaeota. Beta-diversity analyses showed the environmental variations throughout the sampling range to have a stronger impact on the structuring of both the bacterial and archaeal communities than spatial effects. While bacterial communities were significantly influenced by the combined effect of several weakly selective environmental differences, including temperature, archaeal communities appeared to be more uniquely structured by the level of freshly sedimented phytopigments

Barents Sea Drill cuttings research initiative (BARCUT)-project - End report

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Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates

Marine invertebrate microbiomes have been a rich source of bioactive compounds and interesting genomic features. In cases where the achievable amounts of metagenomic DNA are too low for direct sequencing, multiple displacement amplification (MDA) can be used for whole genome amplification. However, MDA has known limitations which can affect the quality of the resulting genomes and metagenomes. In this study, we evaluated the conservation of biosynthetic gene clusters (BGCs) and enzymes in MDA products from low numbers of prokaryotic cells (estimated 2–850). Marine invertebrate microbiomes collected from Arctic and sub-Arctic areas served as source material. The cells were separated from the host tissue, lysed, and directly subjected to MDA. The MDA products were sequenced by Illumina sequencing. Corresponding numbers of bacteria from a set of three reference strains were treated the same way. The study demonstrated that useful information on taxonomic, BGC, and enzyme diversities was obtainable from such marginal quantities of metagenomic material. Although high levels of assembly fragmentation resulted in most BGCs being incomplete, we conclude that this genome mining approach has the potential to reveal interesting BGCs and genes from hard-to-reach biological sources

Seafloor deposition of water-based drill cuttings generates distinctive and lengthy sediment bacterial community changes

The spatial extent and persistence of bacterial change caused by deposition of water-based drill cuttings on the seafloor were explored by a community-wide approach. Ten centimeter sediment cores were sampled along transects extending from ≤15 m to 250 m from three nearby drilling sites in the southern Barents Sea. Eight months, 8 years and 15 years, respectively, had passed since the completion of the drillings. At locations heavily affected by drill cuttings, the two most recent sites showed distinct, corresponding deviances from native Barents Sea bacterial community profiles. Otherwise marginal groups, including Mollicutes and Clostridia, showed significant increases in relative abundance. Beyond 100 m from the boreholes the microbiotas appeared undisturbed, as they did at any distance from the 15-years old borehole. The extent of the biological distortion, as indicated by the present microbial study, agreed with previously published macrofaunal surveys at the same drilling sites

Dynamics of bacterial community exposed to hydrocarbons and oleophilic fertilizer in high-Arctic intertidal beach

Exposure of pristine microbial environments to hydrocarbon contamination stimulates growth of the initially small fraction of indigenous hydrocarbon-degrading bacteria. Custom-made oleophilic fertilizers have been demonstrated to promote oil bioremediation by boosting this proliferation. In the present study, the temporal dynamics of the bacterial community structure and the individual influences of hydrocarbons and an oleophilic fertilizer in shaping the community structure was explored during a 78 days bioremediation experiment in a high-Arctic intertidal beach environment. A combination of cultivation independent 16S rRNA gene length-heterogeneity polymerase chain reaction (LH-PCR) profiling and identification of hydrocarbon-degrading isolates based on partial 16S rRNA gene sequences was employed. LH-PCR community profiles in the fertilizer alone and fertilized kerosene plots were largely indistinguishable throughout the experimental period, while kerosene alone plots showed a markedly different composition of dominant groups. This pointed to the fertilizer as the more decisive factor in shaping the community structure. Most prominent LH-PCR fragments which emerged after kerosene or fertilizer addition could be provisionally assigned to bacterial taxa through coinciding LH-PCR fragment lengths with hydrocarbon degrading isolates obtained from the same type of experimental units. However, a few quantitatively significant LH-PCR groups had no counterparts among the cultivated bacteria. One of these was affiliated to a hitherto unspeciated subgroup within the Alkanindiges/Acinetobacter clade of Moraxellaceae by a 16S rRNA gene cloning approach

Viral assemblage variation in an Arctic shelf seafloor

Spatial differences in microbial communities are observable even in habitats with moderate environmental variation, such as within the pelagic zone or seafloor of geographically finite regions of the oceans. Here we explore whether biogeographical variations are also manifested at this level in the structure of viral assemblages by comparing DNA viromes from the Barents Sea upper seafloor, collected at 5 geographically separated locations. Of the open reading frames, 27 to 44% showed significant similarity to genes of viral genomes in the Refseq database. The majority of the identified open reading frames, i.e. 86 to 95%, were affiliated with sequences of single-stranded DNA (ssDNA) viruses, but the ssDNA virus genetic material was likely strongly overrepresented due to the use of phi29 DNA polymerase for amplifying viral DNA. The majority of ssDNA virus sequences originated from the Microviridae family of phages and the eukaryotic Circular Rep-encoding ssDNA (CRESS-DNA) viruses. The sediment virus assemblages showed higher overall similarity to counterparts from deep-sea sediment of the Pacific Ocean than to, e.g., Arctic Ocean pelagic viromes, supporting the presence of common compositional features in sediment viral assemblages across continental-scale geographical separations. The Barents Sea viromes grouped biogeographically in accordance with the south-north environmental division of this Arctic sea by the oceanic polar front, thereby mirroring a corresponding 16S rRNA gene-based biogeographical division of the bacterial communities. However, compositional differences in the eukaryotic virus assemblages rather than the bacteriophages appeared to be the primary basis for this spatial separation

Microbial trimethylamine-N-oxide as a disease marker: something fishy?

Production of trimethylamine-N-oxide (TMAO) via the gut microbiota has recently been proposed as an important pathophysiological mechanism linking ingestion of ‘unhealthy foods’, such as beef (containing carnitine) and eggs (containing choline), and the development of atherosclerosis. Hence, TMAO has gained attention as a novel biomarker for cardiovascular disease. However, fish and seafood contain considerable amounts of TMAO and are generally accepted as cardioprotective: a puzzling paradox that seems to have been neglected. We suspect that the TMAO story may be a red herring

Perturbation of seafloor bacterial community structure by drilling waste discharge

Offshore drilling operations result in the generation of drill cuttings and localized smothering of the benthic habitats. This study explores bacterial community changes in the in the upper layers of the seafloor resulting from an exploratory drilling operation at 1400 m water depth on the Barents Sea continental slope. Significant restructurings of the sediment microbiota were restricted to the sampling sites notably affected by the drilling waste discharge, i.e. at 30 m and 50 m distances from the drilling location, and to the upper 2 cm of the seafloor. Three bacterial groups, the orders Clostridiales and Desulfuromonadales and the class Mollicutes, were almost exclusively confined to the upper two centimeters at 30 m distance, thereby corroborating an observed increase in anaerobicity inflicted by the drilling waste deposition. The potential of these phylogenetic groups as microbial bioindicators of the spatial extent and persistence of drilling waste discharge should be further explored

From bautasten to bautastor : studies on the Old West Norse word bautasteinn and Swedish words created with bauta(-)

Avhandlingen tar sin utgångspunkt i två uppslagsord i Svenska Akademiens Ordlista 2006: bautasten och bauta-. Övergripande syfte är att beskriva och förklara lexikala förändringar hos ord bildade med bauta(-) i svenskan under perioden 1664–2006, med särskild hänsyn till dessa förändringars relation till ordens etableringsgrad. Materialet består av 838 belägg för ord bildade med baut- eller böt-, och därutöver undersöks 30 ordböcker. Ordet bautasten är ett isländskt lånord i svenskan. Undersökningen av fornvästnordiska ord visar att bautasteinn kan vara ’sten som är slagen ned i jorden’ eller ’sten rest över en fallen krigare’, två betydelser som kan sammanföras i betydelsen ’minnessten’. Denna betydelse framträder också tydligt i samtliga texter. Historiens höga status under stormaktstiden har haft stor betydelse för att ordet bautasten lånades in i svenskan år 1664. Språkstrukturella faktorer har sannolikt lett till att ordet har uppmärksammats och att det har kunnat användas i svenskan. Under perioden 1664–1790 har etableringsgraden hos bautasten inte har varit hög, men vissa tecken tyder på att den höjs under perioden. Fram till ca 1900 stiger etableringsgraden hos bautasten, men den avtar sedan fram till 1973. I avhandlingen antas att ordets växlande etableringsgrad har varit beroende av synen på historien. I början av 1970-talet stiger etableringsgraden åter hos bautasten och 1985 finns första belägget för bauta- som förstärkande förled, vilket med stor sannolikhet har sin orsak att söka hos den stora populariteten hos och spridningen av seriealbumet Asterix. Förleden bauta- har visat sig vara mycket användbar som förstärkande förled. I materialet finns 3 ord bildade med bauta(-) som inte är etablerade i språksamfundet.The starting point for the dissertation is two entry words in Svenska Akademiens Ordlista (SAOL 13, 2006): bautasten and bauta-. The overall purpose is to describe and explain lexical changes in words created with bauta(-) in the Swedish language during 1664–2006, placing particular em¬phasis on these changes in relation to the degree of establish¬ment. The material consists of 838 pieces of evidence of words created with baut- or böt- and, in addition, 30 dictionaries are exam¬ined. The word bautasten (‘menhir’, ‘standing stone’) is an Icelandic loan word in the Swedish lan¬guage. The examination of Old West Norse words shows that bautasteinn can be ’sten som är slagen ned i jorden’ (‘stone beaten into the ground’) or ’sten rest över en fallen krigare’ (‘stone erected over a fallen warrior’), two meanings which can be brought together in the meaning ’minnessten’ (‘memorial monument’). This meaning also clearly appears in all texts. The high status of history during the Swedish Age of Greatness was significant for the inclu¬sion of the word bautasten into the Swedish language in 1664. Language-structural factors have likely lead to the word being noticed as well as made it possible to use in the Swedish language. During 1664–1790, the degree of establishment of bautasten was not high, but there are indi¬cations that it increased during the period. Until about 1900, the degree of estab¬lish¬ment of bautasten increased, but then it decreased up until 1973. In the disserta¬tion it is assumed that the varying degree of establishment has been dependent on the view of history. In the beginning of the 1970s, the degree of establishment of bautasten increased once again and in 1985, the first instance of bauta- as an augmentative prefix appears, which most likely can be attributed to the great popularity and wide spread of the cartoon magazine Asterix. The prefix bauta- has proven to be very usable as an augmentative. There are 3 words created with bauta(-) in the material that are not established in the language communit