Identification and characterization of novel cellulolytic and hemicellulolytic genes and enzymes derived from German grassland soil metagenomes

Nacke, Heiko; Engelhaupt, Martin; Brady, Silja; Fischer, Christian; Tautzt, Janine; Daniel, Rolf

doi:10.1007/s10529-011-0830-2

Cited by 69 publications

(31 citation statements)

References 61 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The enzyme appears to degrade CMC and mixed glucans (lichenan [␤-1,3-␤-1,4] and laminarin [␤-1,3-␤1,6]) but not ␤-1,4-linked xyloglucan. Other metagenome-derived cellulases either fail to degrade laminarin (53)(54)(55)58) or, like the GH5 enzyme described by Liu et al, show very low specific activity (approximately 0.002 U/mg) (59). In agreement with its classification as an endoglucanase, Cell5.1_3 failed, in our assay, to degrade the insoluble substrates Avicel and mannan.…”

Section: Discussionsupporting

confidence: 84%

“…To our knowledge, no cellulase gene has been identified by metagenomics in a marine environment before. All of the cellulases identified by analysis of soil (53)(54)(55)(56) or rumen (57, 58) metagenomes display more than 50% sequence identity to known cellulases, in contrast to our cellulase, which is only 42% identical to the closest known cellulase. Hence, our cellulase appears to be new and only distantly related to known cellulases.…”

Section: Discussionmentioning

confidence: 57%

See 1 more Smart Citation

Identification and Characterization of a Halotolerant, Cold-Active Marine Endo-β-1,4-Glucanase by Using Functional Metagenomics of Seaweed-Associated Microbiota

Martin

Biver

Steels

et al. 2014

Appl Environ Microbiol

View full text Add to dashboard Cite

A metagenomic library was constructed from microorganisms associated with the brown alga Ascophyllum nodosum. Functional screening of this library revealed 13 novel putative esterase loci and two glycoside hydrolase loci. Sequence and gene cluster analysis showed the wide diversity of the identified enzymes and gave an idea of the microbial populations present during the sample collection period. Lastly, an endo-␤-1,4-glucanase having less than 50% identity to sequences of known cellulases was purified and partially characterized, showing activity at low temperature and after prolonged incubation in concentrated salt solutions. Previous surveys have revealed that less than 1% of existing microorganisms can be studied by traditional culturing methods. This leaves most microorganisms and their by-products unknown and unexploited (1, 2) and explains why metagenomics, a culture-independent approach using total microbial genomes from environmental samples, has met with great success over the past decade (3, 4). Sequence-based metagenomics has already provided information about the composition, organization, function, and hierarchy of microbial communities in particular habitats (5). On the other hand, functional genomics applied to metagenomic libraries from diverse environments has led to the discovery of many new enzymes and bioactive compounds and to substantial enrichment of genome databases. To date, most of the enzymes brought to light through metagenomics have been derived from soil (6-9) and gut (10-13) samples.Marine microorganisms represent promising candidate sources of original biocatalysts, as they are exposed to extreme conditions of temperature, pressure, salinity, nutrient availability, etc. Hence, functional screening of marine microbial populations should yield new enzymes with specific and unique physiological and biochemical properties, produced by organisms far different from those usually described in terrestrial environments (14). New enzymes have already been identified in marine metagenomic libraries from seawater samples (15, 16) and from microorganisms in symbiosis with marine organisms such as sponges and corals (17). To our knowledge, however, nobody has yet performed functional screening of metagenomic libraries from algal microbial communities. As algal microbial biofilms are in constant interaction with algal biomass, they represent an interesting source of enzymes and other active compounds (18). Sequence-based studies have already revealed the importance and functions of microbial communities living on the surfaces of algae, showing tight interdependence between algae and their biofilms (19-21). Furthermore, many genes coding for enzymes involved in hydrolyzing algal biomass, such as cellulases, xylanases, ␣-amylases, and specific algal polysaccharidases (e.g., agarases, carrageenases, and alginate lyases), have been identified from cultivable marine bacteria (22,23). Only a few such enzymes have been found in marine metagenomes by functional screening. For example, no cellulase gene...

show abstract

Section: Discussionsupporting

confidence: 84%

Section: Discussionmentioning

confidence: 57%

Identification and Characterization of a Halotolerant, Cold-Active Marine Endo-β-1,4-Glucanase by Using Functional Metagenomics of Seaweed-Associated Microbiota

Martin

Biver

Steels

et al. 2014

Appl Environ Microbiol

View full text Add to dashboard Cite

show abstract

“…Forest soils are among the most diverse microbial habitats on Earth, in which bacteria are the most abundant group of microorganisms (4,85). Forest soils are characterized by a sharp vertical stratification resulting from the decomposition of litter-derived organic matter and the weathering of the mineral matrix.…”

Section: Bacteria In Forest Soilsmentioning

confidence: 99%

Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change

Lladó

López-Mondéjar

Baldrián

2017

Microbiol Mol Biol Rev

527

302

View full text Add to dashboard Cite

The ecology of forest soils is an important field of research due to the role of forests as carbon sinks. Consequently, a significant amount of information has been accumulated concerning their ecology, especially for temperate and boreal forests. Although most studies have focused on fungi, forest soil bacteria also play important roles in this environment. In forest soils, bacteria inhabit multiple habitats with specific properties, including bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are shaped by nutrient availability and biotic interactions. Bacteria contribute to a range of essential soil processes involved in the cycling of carbon, nitrogen, and phosphorus. They take part in the decomposition of dead plant biomass and are highly important for the decomposition of dead fungal mycelia. In rhizospheres of forest trees, bacteria interact with plant roots and mycorrhizal fungi as commensalists or mycorrhiza helpers. Bacteria also mediate multiple critical steps in the nitrogen cycle, including N fixation. Bacterial communities in forest soils respond to the effects of global change, such as climate warming, increased levels of carbon dioxide, or anthropogenic nitrogen deposition. This response, however, often reflects the specificities of each studied forest ecosystem, and it is still impossible to fully incorporate bacteria into predictive models. The understanding of bacterial ecology in forest soils has advanced dramatically in recent years, but it is still incomplete. The exact extent of the contribution of bacteria to forest ecosystem processes will be recognized only in the future, when the activities of all soil community members are studied simultaneously.

show abstract

“…Although traditional cellulose requires acid conditions, newly reported versions including the Xyn01 strain operate at physiological pH [53]. More likely however, is further modification of the sugar backbone that retains the optical properties, but with more obvious routes of clearance from the body.…”

Section: Discussionmentioning

confidence: 99%

Cellulose nanoparticles are a biodegradable photoacoustic contrast agent for use in living mice

et al. 2014

View full text Add to dashboard Cite

Molecular imaging with photoacoustic ultrasound is an emerging field that combines the spatial and temporal resolution of ultrasound with the contrast of optical imaging. However, there are few imaging agents that offer both high signal intensity and biodegradation into small molecules. Here we describe a cellulose-based nanoparticle with peak photoacoustic signal at 700 nm and an in vitro limit of detection of 6 pM (0.02 mg/mL). Doses down to 0.35 nM (1.2 mg/mL) were used to image mouse models of ovarian cancer. Most importantly, the nanoparticles were shown to biodegrade in the presence of cellulase both through a glucose assay and electron microscopy.

show abstract

Identification and characterization of novel cellulolytic and hemicellulolytic genes and enzymes derived from German grassland soil metagenomes

Cited by 69 publications

References 61 publications

Identification and Characterization of a Halotolerant, Cold-Active Marine Endo-β-1,4-Glucanase by Using Functional Metagenomics of Seaweed-Associated Microbiota

Identification and Characterization of a Halotolerant, Cold-Active Marine Endo-β-1,4-Glucanase by Using Functional Metagenomics of Seaweed-Associated Microbiota

Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change

Cellulose nanoparticles are a biodegradable photoacoustic contrast agent for use in living mice

Contact Info

Product

Resources

About