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  • 1
    Electronic Resource
    Electronic Resource
    Screening for bacterial–fungal associations in a south-eastern US salt marsh using pre-established fungal monocultures (2005)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 54 (2005), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Both bacteria and fungi play critical roles in decomposition processes in many natural environments, yet only rarely have they been studied as an integrated community. We examined whether physical associations exist between individual bacterial and fungal species that co-occur on decaying smooth cordgrass, Spartina alterniflora, in a south-eastern US salt marsh. Fungal-pervaded decaying Spartina was used as “bait” for potential bacterial associates. The bundles (infiltrated with one of three dominant fungal members of the decomposer assemblage, or an autoclaved control) were placed in a salt marsh and collected biweekly for 6 weeks during the first experiment (late summer 2002), and weekly for 3 weeks during the second experiment (early summer 2003). Terminal-restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes was used to track colonization by bacterial taxa in association with the established fungal species. T-RFLP analysis of 18S-to-28S internal transcribed spacer (ITS) regions was used to monitor changes in fungal communities once bundles had been placed in the field. Results from both years were nearly identical, and showed that invasion by fungi other than the bait species was slow, resulting in a virtual fungal monoculture for several weeks into the experiments. Surprisingly, bacterial communities were unaffected by the identity of the fungal bait. Regardless of the fungal species, and even in the absence of prior fungal colonization, bacterial 16S rRNA profiles were remarkably similar. These results suggest that few species-specific associations, either positive or negative, exist between bacterial and fungal members of the Spartina decomposer community during initial colonization.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/j.femsec.2005.03.013
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  • 2
    Electronic Resource
    Electronic Resource
    Identification and characterization of humic substances-degrading bacterial isolates from an estuarine environment (2000)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 34 (2000), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Bacterial isolates were obtained from enrichment cultures containing humic substances extracted from estuarine water using an XAD-8 resin. Eighteen isolates were chosen for phylogenetic and physiological characterization based on numerical importance in serial dilutions of the enrichment culture and unique colony morphology. Partial sequences of the 16S rRNA genes indicated that six of the isolates were associated with the α subclass of Proteobacteria, three with the γ-Proteobacteria, and nine with the Gram-positive bacteria. Ten isolates degraded at least one (and up to six) selected aromatic single-ring compounds. Six isolates showed ability to degrade [14C]humic substances derived from the dominant salt marsh grass in the estuary from which they were isolated (Spartina alterniflora), mineralizing 0.4–1.1% of the humic substances over 4 weeks. A mixture of all 18 isolates did not degrade humic substances significantly faster than any of the individual strains, however, and no isolate degraded humic substances to the same extent as the natural marine bacterial community (3.0%). Similar studies with a radiolabeled synthetic lignin ([β-14C]dehydropolymerisate) showed measurable levels of degradation by all 18 bacteria (3.0–8.8% in 4 weeks), but mineralization levels were again lower than that observed for the natural marine bacterial community (28.2%). Metabolic capabilities of the 18 isolates were highly variable and generally did not map to phylogenetic affiliation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.2000.tb00759.x
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  • 3
    Electronic Resource
    Electronic Resource
    Kinetics of microbial degradation of vascular plant material in two wetland ecosystems (1989)
    Springer
    Oecologia 79 (1989), S. 158-167 
    Details
    ISSN: 1432-1939
    Keywords: Kinetics ; Vascular plants ; Litterbags ; Lignocellulose ; Degradation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Vascular plant decomposition was followed during two different years in one freshwater and one marine wetland in southeastern Georgia, USA, using a modified litterbag technique. Chemical analysis of plant material revealed different rates of decomposition for different components of the plant material (soluble components, α-cellulose, hemicellulose, and lignin) and, further, that rates of decomposition of each component changed over time, such that the specific rate of decay for each fraction decreased as decomposition proceeded. Three mathematical models which differen in their treatment of the biochemical heterogeneity of vascular plant detritus were investigated with regard to their relative abilities to describe decomposition kinetics from the field incubations as well as from laboratory microcosm studies with radiolabeled plant material. A decaying coefficient model, which treats plant detritus as a single component but allows for a decreasing specific decomposition rate as material ages, was most successful in describing kinetics of decomposition. This model accomodates the changes in quality of vascular plant detritus resulting from preferential decomposition of more labile components (e.g., non-lignocellulosic material and holocellulose) and the relative accumulation of more refractory components (e.g., lignin) observed with time. The model also accomodates the potential transformation of various plant components into more refractory compounds (humification) during the decomposition process.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00388472
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  • 4
    Electronic Resource
    Electronic Resource
    Decomposition of lignocellulose from a freshwater macrophyte by aero-aquatic fungi (1992)
    Springer
    Microbial ecology 23 (1992), S. 159-167 
    Details
    ISSN: 1432-184X
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Mineralization of uniformly radiolabeled [14C]lignocellulose and specifically radiolabeled [14C-lignin]lignocellulose from the freshwater sedgeCarex walteriana by five aero-aquatic fungi was investigated. The extent of mineralization varied among the five species from 2.2 to 4.2% for the lignin component and from 3.3 to 20.6% for the polysaccharide component. The extent of mineralization of both lignin and polysaccharide moieties by a mixed culture of the five fungi were generally markedly lower than by pure cultures, possibly due to the production of antimicrobial compounds.Spirosphaera foriformis, the most active strain in lignin as well as in polysaccharide mineralization, degraded ferulic acid faster than p-coumaric acid. Decomposition ofCarex walteriana lignocellulose by this strain resulted in decreased cinnamyl/vanillyl (C/V) and syringyl/vanillyl (S/V) ratios.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00172637
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  • 5
    Electronic Resource
    Electronic Resource
    Contributions of three subsystems of a freshwater marsh to total bacterial secondary productivity (1992)
    Springer
    Microbial ecology 24 (1992), S. 161-170 
    Details
    ISSN: 1432-184X
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Rates of bacterial production were measured in the water column, on the surface of plant detritus, and in the surface sediments of a freshwater marsh in the Okefenokee Swamp, Georgia, USA. Bacterioplankton production rates were not correlated with several measures of quantity and quality of dissolved organic matter, including an index of the relative importance of vascular plant derivatives. Bacterioplankton productivity was high (mean: 63 μg C liter−1 day−1) compared with rates reported for other aquatic ecosystems. Somewhat paradoxically, bacterial productivity on plant detritus (mean: 13 μg C g−1 day−1) and sediments (mean: 15 μg C g−1 day−1) was low relative to other locations. On an a real basis, total bacterial productivity in this marsh ecosystem averaged 22 mg C m−2 day−1, based on sample dates in May 1990 and February 1991. Marsh sediments supported the bulk of the production, accounting for 46% (May) and 88% (February) of the total. The remainder was contributed approximately equally by bacteria in the water column and on accumulated stores of plant detritus.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00174452
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  • 6
    Electronic Resource
    Electronic Resource
    Dynamics of microbial biomass and activity in five habitats of the Okefenokee Swamp ecosystem (1987)
    Springer
    Microbial ecology 14 (1987), S. 203-217 
    Details
    ISSN: 1432-184X
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A variety of freshwater marsh and swamp habitats are found interspersed in a mosaic pattern throughout the Okefenokee Swamp, Georgia, USA. We examined spatial and temporal patterns in standing stocks and activity in the microbial community of five habitats within this heterogeneous ecosystem. Standing stock dynamics were studied by measuring microbial biomass (ATP) and bacterial numbers (AODC) in both water and sediments over a 14 month period. Abundance varied temporally, being generally lower in winter months than in spring and summer months. However, a large proportion of the measured variability was not correlated with temporal patterns in temperature or with bulk nutrient levels. Spatial variability was characteristic of the Okefenokee at a variety of large and small scales. Habitat-level heterogeneity was evident when microbial standing stocks and activity (measured as [14C]lignocellulose mineralization) were compared across the five communities, although abundance differences among sites were restricted to nonwinter months when microbial biomass was high. Spatial variation within habitats was also found; patches of surface sediment with differing microbial activity or abundance were measured at scales from 30 cm to 150 m.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02012941
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  • 7
    Electronic Resource
    Electronic Resource
    Photochemical release of biologically available nitrogen from aquatic dissolved organic matter (1996)
    [s.l.] : Nature Publishing Group
    Nature 381 (1996), S. 404-407 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Aquatic humic substances are organic acids (of molecular masses between 500 and 10,000), operationally defined on the basis of their retention on hydrophobic resins and further categorized as humic acids or fulvic acids based on their solubility at low pH2. Humic substances make up the largest ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/381404a0
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  • 8
    Electronic Resource
    Electronic Resource
    Terrestrial inputs of organic matter to coastal ecosystems: An intercomparison of chemical characteristics and bioavailability (1998)
    Springer
    Biogeochemistry 43 (1998), S. 211-234 
    Details
    ISSN: 1573-515X
    Keywords: elemental composition ; lability ; organic carbon ; organic nitrogen ; rivers
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Geosciences
    Notes: Abstract Dissolved and particulate organic matter (DOM and POM) collected from rivers or groundwater feeding five estuaries along the east and west coasts of the USA were characterized with a variety of biogeochemical techniques and related to bioavailability to estuarine microbes. Surface water was sampled from the Columbia, Satilla, Susquehanna and Parker Rivers and groundwater was sampled from the Childs River. Several geochemical descriptors (percent organic matter of suspended particulate matter, C/N, lignin phenol content, ratio of vanillic acid to vanillin) suggested an ordering of the systems with respect to POM lability: Satilla 〈 Parker 〈 Columbia 〈 Susquehanna. DOC concentrations in these systems ranged from 〈100 μM for the Columbia River to 〉2000 μM for the Satilla River. Elemental analysis of DOM concentrates (〉1000 D) was used to predict organic matter composition and to calculate degree of substrate reduction using two different modeling approaches. Models predicted aliphatic carbon ranging between 43 and 60% and aromatic carbon between 26 and 36%, with aliphatic content lowest in the Satilla and highest in the Columbia River. The degree of substrate reduction of the organic matter concentrates followed a pattern similar to that for aliphatic C, being lowest in the Satilla (3.5) and highest in the Columbia (4.0). Extracellular enzyme activity varied broadly across the systems, but again ordered sites in the same way as did aliphatic content and degree of substrate reduction. Bacterial growth rates ranged from 1.3 ug mg-1 d-1 DOC in the Satilla to 1.7 ug mg-1 d-1 DOC in the Parker River. Bioassays confirmed patterns of dissolved organic matter lability predicted by the chemical models. Between 67% to 75% of the variation in bacterial growth could be explained by differences in organic matter composition.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1006016030299
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  • 9
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    Unraveling the functional dark matter through global metagenomics (2023)
    Nature Research
    Details
    Publication Date: 2024-02-07
    Description: Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database3. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.
    Type: Article , PeerReviewed
    Format: text
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 10
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    The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing (2014)
    PUBLIC LIBRARY SCIENCE
    In:  EPIC3PLoS Biology, PUBLIC LIBRARY SCIENCE, 12(6), pp. e1001889, ISSN: 1544-9173
    Details
    Publication Date: 2014-07-01
    Description: Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
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    PAPER (OA)
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