Abstract:
:Organic matter degradation in marine environments is essential for the recycling of nutrients, especially under conditions of anoxia where organic matter tends to accumulate. However, little is known about the diversity of the microbial communities responsible for the mineralization of organic matter in the absence of oxygen, as well as the factors controlling their activities. Here, we determined the active heterotrophic prokaryotic community in the sulphidic water column of the Black Sea, an ideal model system, where a tight coupling between carbon, nitrogen and sulphur cycles is expected. Active microorganisms degrading both dissolved organic matter (DOM) and protein extracts were determined using quantitative DNA stable isotope probing incubation experiments. These results were compared with the metabolic potential of metagenome-assembled genomes obtained from the water column. Organic matter incubations showed that groups like Cloacimonetes and Marinimicrobia are generalists degrading DOM. Based on metagenomic profiles the degradation proceeds in a potential interaction with members of the Deltaproteobacteria and Chloroflexi Dehalococcoidia. On the other hand, microbes with small genomes like the bacterial phyla Parcubacteria, Omnitrophica and of the archaeal phylum Woesearchaeota, were the most active, especially in protein-amended incubations, revealing the potential advantage of streamlined microorganisms in highly reduced conditions.
journal_name
Environ Microbioljournal_title
Environmental microbiologyauthors
Suominen S,Dombrowski N,Sinninghe Damsté JS,Villanueva Ldoi
10.1111/1462-2920.14902subject
Has Abstractpub_date
2019-12-19 00:00:00eissn
1462-2912issn
1462-2920pub_type
杂志文章abstract::Among human faecal bacteria, many members of the Clostridium leptum subgroup are fibrolytic and butyrate producing microorganisms thereby contributing to processes important to colonic health. Yet this phylogenetic subgroup remains poorly described to date. To improve detection and description of members of the C. lep...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/j.1462-2920.2005.00763.x
更新日期:2005-07-01 00:00:00
abstract::Chemolithoautotrophic nitrite oxidizers of the genus Nitrospira are a monophyletic but diverse group of organisms, are widely distributed in many natural habitats, and play a key role in nitrogen elimination during biological wastewater treatment. Phylogenetic analyses of cloned 16S rRNA genes and fluorescence in situ...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/j.1462-2920.2006.01033.x
更新日期:2006-08-01 00:00:00
abstract::Interactions between phytoplankton and bacteria play major roles in global biogeochemical cycles and oceanic nutrient fluxes. These interactions occur in the microenvironment surrounding phytoplankton cells, known as the phycosphere. Bacteria in the phycosphere use either chemotaxis or attachment to benefit from algal...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.15228
更新日期:2020-11-01 00:00:00
abstract::To determine if different algal viruses (Phycodnaviridae) share common patterns of seasonal abundance, quantitative PCR methods were developed and applied to monitor the abundances of three different viruses in Lake Ontario, Canada over 13 months. Throughout the year, the abundances of two different phycodnavirus polB...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/j.1462-2920.2009.01988.x
更新日期:2009-10-01 00:00:00
abstract::Members of the phylum Acidobacteria are abundant and ubiquitous across soils. We performed a large-scale comparative genome analysis spanning subdivisions 1, 3, 4, 6, 8 and 23 (n = 24) with the goal to identify features to help explain their prevalence in soils and understand their ecophysiology. Our analysis revealed...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.14043
更新日期:2018-03-01 00:00:00
abstract::Acid rain can cause severe effects on soil biota and nutrient biogeochemical cycles in the forest ecosystem, but how plant-symbiotic ectomycorrhizal fungi will modulate the effects remains unknown. Here, we conducted a full factorial field experiment in a Masson pine forest by simultaneously controlling the acidity of...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.14457
更新日期:2019-01-01 00:00:00
abstract::Photosynthesis versus irradiance curves and their associated photosynthetic parameters from different phototrophic biofilms isolated from an extreme acidic environment (Río Tinto, SW, Spain) were studied in order to relate them to their species composition and the physicochemical characteristics of their respective sa...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/j.1462-2920.2011.02506.x
更新日期:2011-08-01 00:00:00
abstract::Raphidiopsis raciborskii is an invasive bloom-forming cyanobacteria with the flexibility to utilize atmospheric and fixed nitrogen. Since nitrogen-fixation has a high requirement for iron as an ezyme cofactor, we hypothesize that iron availability would determine the success of the species under nitrogen-fixing condit...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.15328
更新日期:2021-01-01 00:00:00
abstract::The bacterial diversity of an industrial biofilter used for waste gas abatement in an animal-rendering plant was investigated. A 16S rDNA clone library was generated and 444 clones were screened using computer-aided amplified ribosomal DNA restriction analysis (ARDRA). Of the screened clones, 60.8% showed unique ARDRA...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1046/j.1462-2920.2002.00349.x
更新日期:2002-11-01 00:00:00
abstract::Microbial reduction of soluble selenium (Se) or tellurium (Te) species results in immobilization as elemental forms and this process has been employed in soil bioremediation. However, little is known of direct and indirect fungal interactions with Se-/Te-bearing ores. In this research, the ability of Phoma glomerata t...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.15012
更新日期:2020-06-01 00:00:00
abstract::High-throughput sequencing (HTS) surveys, among the most common approaches currently used in environmental microbiology, require reliable reference databases to be correctly interpreted. The EukRef Initiative (eukref.org) is a community effort to manually screen available small subunit (SSU) rRNA gene sequences and pr...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.14264
更新日期:2018-06-01 00:00:00
abstract::Arctic marine microbes are affected by environmental changes that may ultimately influence their functions in carbon cycling. Here, we investigated in concert the structure and enzymatic activities of pelagic, particle-associated and benthic bacterial communities in the central Arctic Ocean, and used these data to eva...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.14304
更新日期:2018-08-01 00:00:00
abstract::Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus are major contributors to oceanic primary production. The genera are genetically diverse, comprising several known ecotypes or lineages. However, little is known of the distribution of these lineages over large geographic areas. Here, we analysed...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/j.1462-2920.2007.01246.x
更新日期:2007-05-01 00:00:00
abstract::The hair-like cell appendages denoted as type IV pili are crucial for biofilm formation in diverse eubacteria. The protein complex responsible for type IV pilus assembly is homologous with the type II protein secretion complex. In the cyanobacterium Synechococcus elongatus PCC 7942, the gene Synpcc7942_2071 encodes an...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.13814
更新日期:2017-07-01 00:00:00
abstract::There has been a growing interest in the degradation of 2,4,6-trinitrotoluene (TNT) over the last decade, ever since its removal from polluted sites was declared an international environmental priority. Certain aerobic and anaerobic microorganisms are capable of using TNT as an N source, although very few studies have...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/j.1462-2920.2007.01272.x
更新日期:2007-06-01 00:00:00
abstract::Of eight laboratory cultures of marine gamma- and alpha-Proteobacteria tested, growth on glycolate as a sole carbon source was detected for only three species: Pseudomonas stutzeri, Oceanimonas doudoroffii and Roseobacter sp. isolate Y3F. Degenerate polymerase chain reaction (PCR) primers were designed to amplify glcD...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/j.1462-2920.2006.01092.x
更新日期:2006-10-01 00:00:00
abstract::Chloride channel proteins (ClC) are found in living systems where they transport chloride ions across cell membranes. Recently, the structure/function of two prokaryotic ClC has been determined but little is known about the role of these proteins in the microbial metabolism of chlorinated compounds. Here we show that ...
journal_title:Environmental microbiology
pub_type: 杂志文章,收录出版
doi:10.1111/j.1462-2920.2006.01136.x
更新日期:2007-01-01 00:00:00
abstract::Located in the Northern Territory of Australia, Ranger uranium mine is directly adjacent to the UNESCO World Heritage listed Kakadu National Park, with rehabilitation targets needed to ensure the site can be incorporated into the park following the mine's closure in 2026. This study aimed to understand the impact of u...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.13839
更新日期:2017-08-01 00:00:00
abstract::Deep-sea ecosystems, such as cold seeps and hydrothermal vents, have high biomass, even though they are located in the benthic zone, where no sunlight is present to provide energy for organism proliferation. Based on the coexistence of the reduced gases and chemoautotrophic microbes, it is inferred that the energy fro...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.15347
更新日期:2020-12-07 00:00:00
abstract::Concatenated sequence analysis with 16S rRNA, rpoB and fusA genes identified a bacterial strain (IRBG74) isolated from root nodules of the aquatic legume Sesbania cannabina as a close relative of the plant pathogen Rhizobium radiobacter (syn. Agrobacterium tumefaciens). However, DNA:DNA hybridization with R. radiobact...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/j.1462-2920.2009.01975.x
更新日期:2009-10-01 00:00:00
abstract::Toxin-antitoxin (TA) systems are small genetic modules usually consisting of two elements-a toxin and an antitoxin. The abundance of TA systems among various bacterial strains may indicate an important evolutionary role. Pseudomonas aeruginosa, which can be found in a variety of niches in nature, is an opportunistic p...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.15102
更新日期:2020-12-01 00:00:00
abstract::The frequent production of the hepatotoxin microcystin (MC) and its impact on the lifestyle of bloom-forming cyanobacteria are poorly understood. Here, we report that MC interferes with the assembly and the subcellular localization of RubisCO, in Microcystis aeruginosa PCC7806. Immunofluorescence, electron microscopic...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.14837
更新日期:2019-12-01 00:00:00
abstract::The ability of the product of a desired reaction to activate a bacterial transcriptional regulator was exploited to develop genetic traps that render the catalytic activity born by a DNA clone into a selectable/scorable phenotype. We established this strategy with a system to expose the activity of dehydrochlorinases ...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/j.1462-2920.2006.00983.x
更新日期:2006-03-01 00:00:00
abstract::Mercury (Hg) is a highly toxic and widely distributed heavy metal, which some Bacteria and Archaea detoxify by the reduction of ionic Hg (Hg[II]) to the elemental volatile form, Hg(0). This activity is specified by the mer operon. The mer operon of the deeply branching thermophile Thermus thermophilus HB27 encodes for...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.14953
更新日期:2020-04-01 00:00:00
abstract::The d- and l-forms of lactate are important fermentation metabolites produced by intestinal bacteria but are found to negatively affect mucosal barrier function and human health. Both enantiomers of lactate can be converted with acetate into the presumed beneficial butyrate by a phylogenetically related group of anaer...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.15269
更新日期:2020-11-01 00:00:00
abstract::Trichodesmium spp. play key roles in global carbon and nitrogen budgets and thus defining what controls their productivity is important for understanding climate change. While iron availability has been shown to be an important chemical factor for controlling both growth and nitrogen fixation rates in Trichodesmium, a...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/j.1462-2920.2009.02026.x
更新日期:2010-01-01 00:00:00
abstract::The spatial organization of gut microorganisms is important with respect to their functional role in the gut ecosystem. Regional differences in the longitudinal and lateral direction are, however, not frequently studied, given the difficulty to sample these human gut regions in vivo. Particularly the insoluble food pa...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.14381
更新日期:2018-09-01 00:00:00
abstract::Reactive oxygen species (ROS) play an important role during host-pathogen interactions and are often an indication of induced host defence responses. In this study, we demonstrate for the first time that Puccinia triticina (Pt) generates ROS, including superoxide, H2 O2 and hydroxyl radicals, during wheat infection. T...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/1462-2920.15063
更新日期:2020-07-01 00:00:00
abstract::Two cellulose-fermenting methanogenic enrichment cultures originating from rice soil, one at 15 degrees C with Methanosaeta and the other at 30 degrees C with Methanosarcina as the dominant acetoclastic methanogen, both degraded cellulose anaerobically via propionate, acetate and H2 to CH4. The degradation was a two-s...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1046/j.1462-2920.2001.00199.x
更新日期:2001-06-01 00:00:00
abstract::The marine gamma-Proteobacterium Alcanivorax borkumensis is highly specialized in the assimilation of aliphatic hydrocarbons, and makes up a large part of the biomass in oil-polluted marine environments. In addition to the previously identified alkane hydroxylase AlkB1, a second alkane hydroxylase (AlkB2) showing 65% ...
journal_title:Environmental microbiology
pub_type: 杂志文章
doi:10.1111/j.1462-2920.2004.00567.x
更新日期:2004-03-01 00:00:00