Functional diversity of bacterial genes associated with aromatic hydrocarbon degradation in anthropogenic dark earth of Amazonia

The objective of this work was to evaluate the catabolic gene diversity for the bacterial degradation of aromatic hydrocarbons in anthropogenic dark earth of Amazonia (ADE) and their biochar (BC). Functional diversity analyses in ADE soils can provide information on how adaptive microorganisms may influence the fertility of soils and what is their involvement in biogeochemical cycles. For this, clone libraries containing the gene encoding for the alpha subunit of aromatic ring-hydroxylating dioxygenases (α-ARHD bacterial gene) were constructed, totaling 800 clones. These libraries were prepared from samples of an ADE soil under two different land uses, located at the Caldeirão Experimental Station - secondary forest (SF) and agriculture (AG) -, and the biochar (SF_BC and AG_BC, respectively). Heterogeneity estimates indicated greater diversity in BC libraries; and Venn diagrams showed more unique operational protein clusters (OPC) in the SF_BC library than the ADE soil, which indicates that specific metabolic processes may occur in biochar. Phylogenetic analysis showed unidentified dioxygenases in ADE soils. Libraries containing functional gene encoding for the alpha subunit of the aromatic ring-hydroxylating dioxygenases (ARHD) gene from biochar show higher diversity indices than those of ADE under secondary forest and agriculture.

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Biochemical effects of mutations in the gene encoding the alpha subunit of eukaryotic initiation factor (eIF) 2B associated with Vanishing White Matter disease

BMC Medical Genetics ◽

10.1186/s12881-015-0204-z ◽

2015 ◽

Vol 16 (1) ◽

Cited By ~ 9

Author(s):

Noel C. Wortham ◽

Christopher G. Proud

Keyword(s):

White Matter ◽

Initiation Factor ◽

Alpha Subunit ◽

White Matter Disease ◽

Eukaryotic Initiation Factor ◽

Gene Encoding ◽

Biochemical Effects ◽

Vanishing White Matter Disease ◽

Vanishing White Matter

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Microbial Functional Gene Diversity with a Shift of Subsurface Redox Conditions duringIn SituUranium Reduction

Applied and Environmental Microbiology ◽

10.1128/aem.06528-11 ◽

2012 ◽

Vol 78 (8) ◽

pp. 2966-2972 ◽

Cited By ~ 35

Author(s):

Yuting Liang ◽

Joy D. Van Nostrand ◽

Lucie A. N′Guessan ◽

Aaron D. Peacock ◽

Ye Deng ◽

...

Keyword(s):

Functional Diversity ◽

Field Experiments ◽

Gene Diversity ◽

Functional Gene ◽

Redox Conditions ◽

Functional Genes ◽

Microbial Functional Diversity ◽

Content Type ◽

Microbial Functional Gene

ABSTRACTTo better understand the microbial functional diversity changes with subsurface redox conditions duringin situuranium bioremediation, key functional genes were studied with GeoChip, a comprehensive functional gene microarray, in field experiments at a uranium mill tailings remedial action (UMTRA) site (Rifle, CO). The results indicated that functional microbial communities altered with a shift in the dominant metabolic process, as documented by hierarchical cluster and ordination analyses of all detected functional genes. The abundance ofdsrABgenes (dissimilatory sulfite reductase genes) and methane generation-relatedmcrgenes (methyl coenzyme M reductase coding genes) increased when redox conditions shifted from Fe-reducing to sulfate-reducing conditions. The cytochrome genes detected were primarily fromGeobactersp. and decreased with lower subsurface redox conditions. Statistical analysis of environmental parameters and functional genes indicated that acetate, U(VI), and redox potential (Eh) were the most significant geochemical variables linked to microbial functional gene structures, and changes in microbial functional diversity were strongly related to the dominant terminal electron-accepting process following acetate addition. The study indicates that the microbial functional genes clearly reflect thein situredox conditions and the dominant microbial processes, which in turn influence uranium bioreduction. Microbial functional genes thus could be very useful for tracking microbial community structure and dynamics during bioremediation.

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Vertical dynamics in community functioning of biofilm-dwelling ciliates during the colonisation process in coastal waters of the Yellow Sea

Marine and Freshwater Research ◽

10.1071/mf18448 ◽

2019 ◽

Vol 70 (11) ◽

pp. 1611 ◽

Cited By ~ 8

Author(s):

Xiaoyun Bai ◽

Congcong Guo ◽

Mamun Abdullah Al ◽

Alan Warren ◽

Henglong Xu

Keyword(s):

Functional Diversity ◽

Functional Traits ◽

Coastal Waters ◽

Yellow Sea ◽

Northern China ◽

Diversity Indices ◽

Functional Trait ◽

The Yellow Sea ◽

Biological Traits ◽

Trait Distribution

Multifunctional trait analysis is increasingly recognised as an effective tool for assessing ecosystem function and environmental quality. Here, a baseline study was performed at four depths (i.e. 1, 2, 3.5 and 5m) in Yellow Sea coastal waters of northern China in order to determine the optimal depth for bioassessment using biological traits of biofilm-dwelling ciliates. Community-weighted means (CWM) from functional traits system were used to summarise the trait distribution and functional diversity of ciliates among the four depths during a 1-month colonisation period. Functional trait distribution revealed a clear temporal variation among the four depths. In total, 3 of 17 functional traits (i.e. feeding type, body size and flexibility) showed significant temporal patterns. Bootstrapped averaging and permutational multivariate analysis of variance (PERMANOVA) tests demonstrated that the colonisation pattern of biofilm-dwelling ciliates as expressed by CWM at 1 and 2m differed significantly from those at 3.5 and 5m. Functional diversity indices showed lower variability at 1 and 2m than at 3.5 and 5m. These results suggest that 1 and 2m are the preferred sampling depths for bioassessment of marine water quality using biological traits of biofilm-dwelling ciliates.

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FUNCTIONAL DIVERSITY AND ITS ATTRIBUTE FACTORS IN THE YUNMENG MOUNTAIN NATIONAL FOREST PARK IN BEIJING, CHINA

CERNE ◽

10.1590/01047760201723012264 ◽

2017 ◽

Vol 23 (1) ◽

pp. 75-84

Author(s):

Jin-Tun Zhang ◽

Xiaohang Bai ◽

Dan Shao

Keyword(s):

Functional Diversity ◽

Altitudinal Gradient ◽

Soil Depth ◽

Functional Divergence ◽

Diversity Indices ◽

Slope Position ◽

National Forest ◽

Forest Communities ◽

Forest Park ◽

Functional Diversity Indices

ABSTRACT The interaction of diversity with environmental gradients is an important topic in ecology. This study investigated the pattern of change in functional diversity in forest communities along an altitudinal gradient in Yunmeng Mountain National Forest Park, China. Forty-two quadrats measuring 10 x 10 m in the forest communities were set up along this altitudinal gradient; plant species, traits and environmental variables were measured and recorded. Six functional diversity indices, namely, Modified functional attribute diversity (MFAD), Functional diversity plot-based dendrogram index (FDp), Functional diversity community-based dendrogram index (FDc), Functional evenness (FEve), Functional divergence (FDiv) and Functional dispersion (FDis), were used to calculate functional diversity. The results showed that functional diversity varied greatly in forest communities in the Yunmeng Mountain Forest Park. Functional diversity was significantly correlated with elevation and slope position and somewhat correlated with soil depth. Functional diversity increased with an increase in the elevation and decreased as the slope position changed from valley bottom to hill ridge. Functional diversity was closely related to species richness. The six functional diversity indices were all applicable to functional diversity studies of forest communities.

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MxaF gene, a gene encoding alpha subunit of methanol dehydrogenase in and false growth of acetic acid bacteria on methanol

The Journal of General and Applied Microbiology ◽

10.2323/jgam.55.101 ◽

2009 ◽

Vol 55 (2) ◽

pp. 101-110 ◽

Cited By ~ 5

Author(s):

Rei Suzuki ◽

Puspita Lisdiyanti ◽

Kazuo Komagata ◽

Tai Uchimura

Keyword(s):

Acetic Acid ◽

Acetic Acid Bacteria ◽

Methanol Dehydrogenase ◽

Alpha Subunit ◽

Gene Encoding

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Epoxy Coenzyme A Thioester Pathways for Degradation of Aromatic Compounds

Applied and Environmental Microbiology ◽

10.1128/aem.00633-12 ◽

2012 ◽

Vol 78 (15) ◽

pp. 5043-5051 ◽

Cited By ~ 19

Author(s):

Wael Ismail ◽

Johannes Gescher

Keyword(s):

Aromatic Ring ◽

Aromatic Compounds ◽

Coenzyme A ◽

Environmental Pollutants ◽

Bacterial Degradation ◽

Ring Cleavage ◽

The Novel ◽

Energy Consuming ◽

Coa Thioesters ◽

Hydrolytic Mechanism

ABSTRACTAromatic compounds (biogenic and anthropogenic) are abundant in the biosphere. Some of them are well-known environmental pollutants. Although the aromatic nucleus is relatively recalcitrant, microorganisms have developed various catabolic routes that enable complete biodegradation of aromatic compounds. The adopted degradation pathways depend on the availability of oxygen. Under oxic conditions, microorganisms utilize oxygen as a cosubstrate to activate and cleave the aromatic ring. In contrast, under anoxic conditions, the aromatic compounds are transformed to coenzyme A (CoA) thioesters followed by energy-consuming reduction of the ring. Eventually, the dearomatized ring is opened via a hydrolytic mechanism. Recently, novel catabolic pathways for the aerobic degradation of aromatic compounds were elucidated that differ significantly from the established catabolic routes. The new pathways were investigated in detail for the aerobic bacterial degradation of benzoate and phenylacetate. In both cases, the pathway is initiated by transforming the substrate to a CoA thioester and all the intermediates are bound by CoA. The subsequent reactions involve epoxidation of the aromatic ring followed by hydrolytic ring cleavage. Here we discuss the novel pathways, with a particular focus on their unique features and occurrence as well as ecological significance.

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Genetic differentiation of the neotropical tree species Protium spruceanum (Benth.) Engler (Burseraceae) between fragments and vegetation corridors in Brazilian Atlantic forest

Acta Botanica Brasilica ◽

10.1590/s0102-33062009000400028 ◽

2009 ◽

Vol 23 (4) ◽

pp. 1180-1185 ◽

Cited By ~ 2

Author(s):

Fábio de Almeida Vieira ◽

Dulcinéia de Carvalho

Keyword(s):

Genetic Differentiation ◽

Secondary Forest ◽

Gene Diversity ◽

Isolation By Distance ◽

Neotropical Tree ◽

Second Growth ◽

Human Habitat ◽

Protium Spruceanum ◽

Allozyme Loci ◽

Vegetation Corridors

We studied patterns of genetic differentiation in a connected landscape with an interesting history of human habitat conversion that began two centuries ago, during the Brazilian colonization period. In the fragments of Brazilian Atlantic seasonal forest and corridors of secondary forest, Protium spruceanum is an abundant native, mass-flowering/insect-pollinated and bird-dispersed tree. Genetic diversity was analyzed from 230 individuals in five fragments (1 to 11.8 ha) and four corridors (460 to 1000 m length) using allozyme loci. We did not find evidence of inbreeding within fragments or corridors, but the proportion of heterozygotes (<IMG SRC="/img/revistas/abb/v23n4/a28simb1.gif" WIDTH=287 HEIGHT=96>) were significantly higher in fragments than in the secondary vegetation corridors, based on Goudet's G-test (P = 0.036). Genetic differentiation was low and no pattern of isolation by distance was detected. All fragments generally present low historical genetic differentiation with corridors that they are connected, indicating possible gene flow via seeds and pollen. Due to the consistently low differentiation observed among them and the absence of a significant reduction in gene diversity in second-growth forests, we conclude that corridors of second-growth forests would be an important alternative in the genetic connection of isolated forest fragments.

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