scholarly journals Bacterial and fungal contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing

2018 ◽  
Author(s):  
Roland C. Wilhelm ◽  
Rahul Singh ◽  
Lindsay D. Eltis ◽  
William W. Mohn
Keyword(s):  
Stable Isotope ◽  
Forest Soils ◽  
Cellulose Degradation ◽  
Stable Isotope Probing ◽  
Bacterial Degradation ◽  
Lignocellulose Degradation ◽  
Shotgun Metagenomics ◽  
Catabolic Genes ◽  
Degrading Bacteria ◽  
Bacteria And Fungi

AbstractDelignification, or lignin-modification, facilitates the decomposition of lignocellulose in woody plant biomass. The extant diversity of lignin-degrading bacteria and fungi is underestimated by culture-dependent methods, limiting our understanding of the functional and ecological traits of decomposers populations. Here, we describe the use of stable isotope probing (SIP) coupled with amplicon and shotgun metagenomics to identify and characterize the functional attributes of lignin-, cellulose-and hemicellulose-degrading fungi and bacteria in coniferous forest soils from across North America. We tested the extent to which catabolic genes partitioned among different decomposer taxa; the relative roles of bacteria and fungi, and whether taxa or catabolic genes correlated with variation in lignocellulolytic activity, measured as the total assimilation of13C-label into DNA and phospholipid fatty acids. We found high overall bacterial degradation of our model lignin substrate, particularly by gram-negative bacteria (Comamonadaceae and Caulobacteraceae), while fungi were more prominent in cellulose-degradation. Very few taxa incorporated13C-label from more than one lignocellulosic polymer, suggesting specialization among decomposers. Collectively, members of Caulobacteraceae could degrade all three lignocellulosic polymers, providing new evidence for their importance in lignocellulose degradation. Variation in lignin-degrading activity was better explained by microbial community properties, such as catabolic gene content and community structure, than cellulose-degrading activity. SIP significantly improved shotgun metagenome assembly resulting in the recovery of several high-quality draft metagenome-assembled genomes and over 7,500 contigs containing unique clusters of carbohydrate-active genes. These results improve understanding of which organisms, conditions and corresponding functional genes contribute to lignocellulose decomposition.

scholarly journals Poplar phyllosphere harbors disparate isoprene-degrading bacteria

2018 ◽  
Vol 115 (51) ◽  
pp. 13081-13086 ◽  
Author(s):  
Andrew T. Crombie ◽  
Nasmille L. Larke-Mejia ◽  
Helen Emery ◽  
Robin Dawson ◽  
Jennifer Pratscher ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Sole Source ◽  
Stable Isotope Probing ◽  
Shotgun Metagenomics ◽  
Gram Positive Bacteria ◽  
Metabolic Genes ◽  
Biological Cycling ◽  
Degrading Bacteria ◽  
Soils And Sediments ◽  
Poplar Tree

The climate-active gas isoprene (2-methyl-1,3-butadiene) is released to the atmosphere in huge quantities, almost equaling that of methane, yet we know little about the biological cycling of isoprene in the environment. Although bacteria capable of growth on isoprene as the sole source of carbon and energy have previously been isolated from soils and sediments, no microbiological studies have targeted the major source of isoprene and examined the phyllosphere of isoprene-emitting trees for the presence of degraders of this abundant carbon source. Here, we identified isoprene-degrading bacteria in poplar tree-derived microcosms by DNA stable isotope probing. The genomes of isoprene-degrading taxa were reconstructed, putative isoprene metabolic genes were identified, and isoprene-related gene transcription was analyzed by shotgun metagenomics and metatranscriptomics. Gram-positive bacteria of the genusRhodococcusproved to be the dominant isoprene degraders, as previously found in soil. However, a wider diversity of isoprene utilizers was also revealed, notablyVariovorax, a genus not previously associated with this trait. This finding was confirmed by expression of the isoprene monooxygenase fromVariovoraxin a heterologous host. AVariovoraxstrain that could grow on isoprene as the sole carbon and energy source was isolated. Analysis of its genome confirmed that it contained isoprene metabolic genes with an identical layout and high similarity to those identified by DNA-stable isotope probing and metagenomics. This study provides evidence of a wide diversity of isoprene-degrading bacteria in the isoprene-emitting tree phyllosphere and greatly enhances our understanding of the biodegradation of this important metabolite and climate-active gas.

scholarly journals Identifying the Active Microbiome Associated with Roots and Rhizosphere Soil of Oilseed Rape

2017 ◽  
Vol 83 (22) ◽  
Author(s):  
Konstantia Gkarmiri ◽  
Shahid Mahmood ◽  
Alf Ekblad ◽  
Sadhna Alström ◽  
Nils Högberg ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Stable Isotope ◽  
Oilseed Rape ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Rhizosphere Soil ◽  
Stable Isotope Probing ◽  
Biofuel Production ◽  
Content Type ◽  
Bacteria And Fungi

ABSTRACT RNA stable isotope probing and high-throughput sequencing were used to characterize the active microbiomes of bacteria and fungi colonizing the roots and rhizosphere soil of oilseed rape to identify taxa assimilating plant-derived carbon following 13CO2 labeling. Root- and rhizosphere soil-associated communities of both bacteria and fungi differed from each other, and there were highly significant differences between their DNA- and RNA-based community profiles. Verrucomicrobia, Proteobacteria, Planctomycetes, Acidobacteria, Gemmatimonadetes, Actinobacteria, and Chloroflexi were the most active bacterial phyla in the rhizosphere soil. Bacteroidetes were more active in roots. The most abundant bacterial genera were well represented in both the 13C- and 12C-RNA fractions, while the fungal taxa were more differentiated. Streptomyces, Rhizobium, and Flavobacterium were dominant in roots, whereas Rhodoplanes and Sphingomonas (Kaistobacter) were dominant in rhizosphere soil. “Candidatus Nitrososphaera” was enriched in 13C in rhizosphere soil. Olpidium and Dendryphion were abundant in the 12C-RNA fraction of roots; Clonostachys was abundant in both roots and rhizosphere soil and heavily 13C enriched. Cryptococcus was dominant in rhizosphere soil and less abundant, but was 13C enriched in roots. The patterns of colonization and C acquisition revealed in this study assist in identifying microbial taxa that may be superior competitors for plant-derived carbon in the rhizosphere of Brassica napus. IMPORTANCE This microbiome study characterizes the active bacteria and fungi colonizing the roots and rhizosphere soil of Brassica napus using high-throughput sequencing and RNA-stable isotope probing. It identifies taxa assimilating plant-derived carbon following 13CO2 labeling and compares these with other less active groups not incorporating a plant assimilate. Brassica napus is an economically and globally important oilseed crop, cultivated for edible oil, biofuel production, and phytoextraction of heavy metals; however, it is susceptible to several diseases. The identification of the fungal and bacterial species successfully competing for plant-derived carbon, enabling them to colonize the roots and rhizosphere soil of this plant, should enable the identification of microorganisms that can be evaluated in more detailed functional studies and ultimately be used to improve plant health and productivity in sustainable agriculture.

scholarly journals Novel Phenanthrene-Degrading Bacteria Identified by DNA-Stable Isotope Probing

PLoS ONE ◽  
2015 ◽  
Vol 10 (6) ◽  
pp. e0130846 ◽  
Author(s):  
Longfei Jiang ◽  
Mengke Song ◽  
Chunling Luo ◽  
Dayi Zhang ◽  
Gan Zhang
Keyword(s):  
Stable Isotope ◽  
Stable Isotope Probing ◽  
Degrading Bacteria

scholarly journals Molecular Characterization of Low-Density Polyethene (LDPE) Degrading Bacteria and Fungi from Dandora Dumpsite, Nairobi, Kenya

2018 ◽  
Vol 2018 ◽  
pp. 1-10 ◽  
Author(s):  
Christabel Ndahebwa Muhonja ◽  
Gabriel Magoma ◽  
Mabel Imbuga ◽  
Huxley Mae Makonde
Keyword(s):  
Bacillus Cereus ◽  
Aspergillus Oryzae ◽  
Bacterial Degradation ◽  
Low Density ◽  
Optimum Growth ◽  
Alkane Hydroxylase ◽  
Fungal Isolates ◽  
Degrading Bacteria ◽  
Bacteria And Fungi

This study aimed at molecular and biochemical characterization of low-density polyethene (LDPE) degrading fungi and bacteria from Dandora dumpsite, Nairobi. Twenty bacterial and 10 fungal isolates were identified using 16S rDNA and 18S rDNA sequences for bacteria and fungi, respectively. The highest fungal degradation was attributed to Aspergillus oryzae strain A5,1 while the highest bacterial degradation was attributed to Bacillus cereus strain A5,a and Brevibacillus borstelensis strain B2,2, respectively. Isolates were screened for their ability to produce extracellular laccase and esterase; Aspergillus fumigatus strain B2,2 exhibited the highest presence of laccase (15.67 mm) while Aspergillus oryzae strain A5,1 exhibited the highest presence of esterase (14.33 mm). Alkane hydroxylase-encoding genes were screened for using primer AlkB 1 which amplified the fragment of size 870 bp. Four bacterial samples were positive for the gene. Optimum growth temperature of the fungal isolates was 30°C. The possession of laccase, esterase, and alkane hydroxylase activities is suggested as key molecular basis for LDPE degrading capacity. Knowledge of optimum growth conditions will serve to better utilize microbes in the bioremediation of LDPE. The application of Aspergillus oryzae strain A5,1 and Bacillus cereus strain A5,a in polyethene degradation is a promising option in this kind of bioremediation as they exhibited significantly high levels of biodegradation. Further investigation of more alkane degrading genes in biodegrading microbes will inform the choice of the right microbial consortia for bioaugmentation strategies.

scholarly journals Identification of Benzo[a]pyrene-Metabolizing Bacteria in Forest Soils by Using DNA-Based Stable-Isotope Probing

2015 ◽  
Vol 81 (21) ◽  
pp. 7368-7376 ◽  
Author(s):  
Mengke Song ◽  
Chunling Luo ◽  
Longfei Jiang ◽  
Dayi Zhang ◽  
Yujie Wang ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Forest Soils ◽  
Contaminated Soils ◽  
Stable Isotope Probing ◽  
Soil Microcosms ◽  
Content Type ◽  
The Family ◽  
Polycyclic Aromatic ◽  
Uncultivated Bacteria ◽  
Different Soils

ABSTRACTDNA-based stable-isotope probing (DNA-SIP) was used in this study to investigate the uncultivated bacteria with benzo[a]pyrene (BaP) metabolism capacities in two Chinese forest soils (Mt. Maoer in Heilongjiang Province and Mt. Baicaowa in Hubei Province). We characterized three different phylotypes with responsibility for BaP degradation, none of which were previously reported as BaP-degrading microorganisms by SIP. In Mt. Maoer soil microcosms, the putative BaP degraders were classified as belonging to the genusTerrimonas(familyChitinophagaceae, orderSphingobacteriales), whereasBurkholderiaspp. were the key BaP degraders in Mt. Baicaowa soils. The addition of metabolic salicylate significantly increased BaP degradation efficiency in Mt. Maoer soils, and the BaP-metabolizing bacteria shifted to the microorganisms in the familyOxalobacteraceae(genus unclassified). Meanwhile, salicylate addition did not change either BaP degradation or putative BaP degraders in Mt. Baicaowa. Polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHD) genes were amplified, sequenced, and quantified in the DNA-SIP13C heavy fraction to further confirm the BaP metabolism. By illuminating the microbial diversity and salicylate additive effects on BaP degradation across different soils, the results increased our understanding of BaP natural attenuation and provided a possible approach to enhance the bioremediation of BaP-contaminated soils.

scholarly journals Isolation of isoprene degrading bacteria from soils, development ofisoAgene probes and identification of the active isoprene-degrading soil community using DNA-stable isotope probing

2016 ◽  
Vol 18 (8) ◽  
pp. 2743-2753 ◽  
Author(s):  
Myriam El Khawand ◽  
Andrew T. Crombie ◽  
Antonia Johnston ◽  
Dmitrii V. Vavlline ◽  
Joseph C. McAuliffe ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Stable Isotope Probing ◽  
Soil Community ◽  
Degrading Bacteria
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