scholarly journals Biome-Level Biogeography of Streambed Microbiota

2008 ◽  
Vol 74 (10) ◽  
pp. 3014-3021 ◽  
Author(s):  
Robert H. Findlay ◽  
Christine Yeates ◽  
Meredith A. J. Hullar ◽  
David A. Stahl ◽  
Louis A. Kaplan
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Biomass ◽  
Bacterial Community ◽  
Microbial Community Structure ◽  
Bacterial Community Structure ◽  
Phospholipid Fatty Acid ◽  
Principal Component ◽  
Community Structures ◽  
Microbial Community Structures

ABSTRACT A field study was conducted to determine the microbial community structures of streambed sediments across diverse geographic and climatic areas. Sediment samples were collected from three adjacent headwater forest streams within three biomes, eastern deciduous (Pennsylvania), southeastern coniferous (New Jersey), and tropical evergreen (Guanacaste, Costa Rica), to assess whether there is biome control of stream microbial community structure. Bacterial abundance, microbial biomass, and bacterial and microbial community structures were determined using classical, biochemical, and molecular methods. Microbial biomass, determined using phospholipid phosphate, was significantly greater in the southeastern coniferous biome, likely due to the smaller grain size, higher organic content, and lower levels of physical disturbance of these sediments. Microbial community structure was determined using phospholipid fatty acid (PLFA) profiles and bacterial community structure from terminal restriction fragment length polymorphism and edited (microeukaryotic PLFAs removed) PLFA profiles. Principal component analysis (PCA) was used to investigate patterns in total microbial community structure. The first principal component separated streams based on the importance of phototrophic microeukaryotes within the community, while the second separated southeastern coniferous streams from all others based on increased abundance of fungal PLFAs. PCA also indicated that within- and among-stream variations were small for tropical evergreen streams and large for southeastern coniferous streams. A similar analysis of bacterial community structure indicated that streams within biomes had similar community structures, while each biome possessed a unique streambed community, indicating strong within-biome control of stream bacterial community structure.

scholarly journals Microbial Population Changes during Bioremediation of an Experimental Oil Spill

1999 ◽  
Vol 65 (8) ◽  
pp. 3566-3574 ◽  
Author(s):  
Sarah J. MacNaughton ◽  
John R. Stephen ◽  
Albert D. Venosa ◽  
Gregory A. Davis ◽  
Yun-Juan Chang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Oil Spill ◽  
Phospholipid Fatty Acid ◽  
Community Structures ◽  
Gram Negative ◽  
Dgge Analysis ◽  
16S Rdna Pcr ◽  
Microbial Community Structures ◽  
Plfa Analysis

ABSTRACT Three crude oil bioremediation techniques were applied in a randomized block field experiment simulating a coastal oil spill. Four treatments (no oil control, oil alone, oil plus nutrients, and oil plus nutrients plus an indigenous inoculum) were applied. In situ microbial community structures were monitored by phospholipid fatty acid (PLFA) analysis and 16S rDNA PCR-denaturing gradient gel electrophoresis (DGGE) to (i) identify the bacterial community members responsible for the decontamination of the site and (ii) define an end point for the removal of the hydrocarbon substrate. The results of PLFA analysis demonstrated a community shift in all plots from primarily eukaryotic biomass to gram-negative bacterial biomass with time. PLFA profiles from the oiled plots suggested increased gram-negative biomass and adaptation to metabolic stress compared to unoiled controls. DGGE analysis of untreated control plots revealed a simple, dynamic dominant population structure throughout the experiment. This banding pattern disappeared in all oiled plots, indicating that the structure and diversity of the dominant bacterial community changed substantially. No consistent differences were detected between nutrient-amended and indigenous inoculum-treated plots, but both differed from the oil-only plots. Prominent bands were excised for sequence analysis and indicated that oil treatment encouraged the growth of gram-negative microorganisms within the α-proteobacteria andFlexibacter-Cytophaga-Bacteroides phylum. α-Proteobacteria were never detected in unoiled controls. PLFA analysis indicated that by week 14 the microbial community structures of the oiled plots were becoming similar to those of the unoiled controls from the same time point, but DGGE analysis suggested that major differences in the bacterial communities remained.

scholarly journals Variations in microbial community structure and functional gene expression in bio-treatment processes with odorous pollutants

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Weidong Li ◽  
Jianguo Ni ◽  
Shaoqin Cai ◽  
Ying Liu ◽  
Chenjia Shen ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Differential Expression Analysis ◽  
Enrichment Analysis ◽  
Community Structures ◽  
Industrial Emissions ◽  
Gas Treatment ◽  
Kegg Pathways ◽  
Microbial Community Structures

AbstractEngineered microbial ecosystems in biofilters have been widely applied to treat odorous gases from industrial emissions. Variations in microbial community structure and function associated with the removal of odorous gases by biofilters are largely unknown. This study performed a metagenomic analysis to discover shifts in microbial community structures in a commercial scale biofilter after treating odorous gas. Our study identified 175,675 functional genes assigned into 43 functional KEGG pathways. Based on the unigene sequences, there were significant changes in microbial community structures in the biofilter after treating odorous gas. The dominant genera were Thiobacillus and Oceanicaulis before the treatment, and were Acidithiobacillus and Ferroplasma after the treatment. A clustering analysis showed that the number of down-regulated microbes exceeded the number of up-regulated microbes, suggesting that odorous gas treatment reduced in microbial community structures. A differential expression analysis identified 29,975 up- and 452,599 down-regulated genes. An enrichment analysis showed 17 classic types of xenobiotic biodegradation pathways. The results identified 16 and 15 genes involved in ammonia and sulfite metabolism, respectively; an analysis of their relative abundance identified several up-regulated genes, which may be efficient genes involved in removing odorous gases. The data provided in this study demonstrate the changes in microbial communities and help identify the dominant microflora and genes that play key roles in treating odorous gases.

scholarly journals Genotypic and Phenotypic Responses of a Riverine Microbial Community to Polycyclic Aromatic Hydrocarbon Contamination

1998 ◽  
Vol 64 (9) ◽  
pp. 3422-3428 ◽  
Author(s):  
Donald E. Langworthy ◽  
Raymond D. Stapleton ◽  
Gary S. Sayler ◽  
Robert H. Findlay
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Nucleic Acid ◽  
Microbial Community Structure ◽  
Phospholipid Fatty Acid ◽  
Principal Component ◽  
Dry Weight ◽  
Hydrocarbon Contamination ◽  
Polycyclic Aromatic ◽  
Nucleic Acid Analysis

ABSTRACT The phenotypic and genotypic adaptation of a freshwater sedimentary microbial community to elevated (22 to 217 μg g [dry weight] of sediment−1) levels of polycyclic aromatic hydrocarbons (PAHs) was determined by using an integrated biomolecular approach. Central to the approach was the use of phospholipid fatty acid (PLFA) profiles to characterize the microbial community structure and nucleic acid analysis to quantify the frequency of degradative genes. The study site was the Little Scioto River, a highly impacted, channelized riverine system located in central Ohio. This study site is a unique lotic system, with all sampling stations having similar flow and sediment characteristics both upstream and downstream from the source of contamination. These characteristics allowed for the specific analysis of PAH impact on the microbial community. PAH concentrations in impacted sediments ranged from 22 to 217 μg g (dry weight) of sediment−1, while PAH concentrations in ambient sediments ranged from below detection levels to 1.5 μg g (dry weight) of sediment−1. Total microbial biomass measured by phospholipid phosphate (PLP) analysis ranged from 95 to 345 nmol of PLP g (dry weight) of sediment−1. Nucleic acid analysis showed the presence of PAH-degradative genes at all sites, although observed frequencies were typically higher at contaminated sites. Principal component analysis of PLFA profiles indicated that moderate to high PAH concentrations altered microbial community structure and that seasonal changes were comparable in magnitude to the effects of PAH pollution. These data indicate that this community responded to PAH contamination at both the phenotypic and the genotypic level.

scholarly journals Soil microbial communities following bush removal in a Namibian savanna

2015 ◽  
Vol 2 (2) ◽  
pp. 1393-1418
Author(s):  
J. S. Buyer ◽  
A. Schmidt-Küntzel ◽  
M. Nghikembua ◽  
J. E. Maul ◽  
L. Marker
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Biomass ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Phospholipid Fatty Acid ◽  
Soil Microbial Communities ◽  
Management Approach ◽  
Polymorphism Analysis ◽  
Soil Microbial

Abstract. Savanna ecosystems are subject to desertification and bush encroachment, which reduce the carrying capacity for wildlife and livestock. Bush thinning is a management approach that can, at least temporarily, restore grasslands and raise the grazing value of the land. In this study we examined the soil microbial communities under bush and grass in Namibia. We analyzed the soil through a chronosequence where bush was thinned at 9, 5, or 3 years before sampling. Soil microbial biomass, the biomass of specific taxonomic groups, and overall microbial community structure was determined by phospholipid fatty acid analysis, while the community structure of Bacteria, Archaea, and fungi was determined by multiplex terminal restriction fragment length polymorphism analysis. Soil under bush had higher pH, C, N, and microbial biomass than under grass, and the microbial community structure was also altered under bush compared to grass. A major disturbance to the ecosystem, bush thinning, resulted in an altered microbial community structure compared to control plots, but the magnitude of this perturbation gradually declined with time. Community structure was primarily driven by pH, C, and N, while vegetation type, bush thinning, and time since bush thinning were of secondary importance.

scholarly journals Soil microbial communities following bush removal in a Namibian savanna

SOIL ◽  
2016 ◽  
Vol 2 (1) ◽  
pp. 101-110 ◽  
Author(s):  
Jeffrey S. Buyer ◽  
Anne Schmidt-Küntzel ◽  
Matti Nghikembua ◽  
Jude E. Maul ◽  
Laurie Marker
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Biomass ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Phospholipid Fatty Acid ◽  
Soil Microbial Communities ◽  
Management Approach ◽  
Polymorphism Analysis ◽  
Soil Microbial

Abstract. Savanna ecosystems are subject to desertification and bush encroachment, which reduce the carrying capacity for wildlife and livestock. Bush thinning is a management approach that can, at least temporarily, restore grasslands and raise the grazing value of the land. In this study we examined the soil microbial communities under bush and grass in Namibia. We analyzed the soil through a chronosequence where bush was thinned at 9, 5, or 3 years before sampling. Soil microbial biomass, the biomass of specific taxonomic groups, and overall microbial community structure was determined by phospholipid fatty acid analysis, while the community structure of Bacteria, Archaea, and fungi was determined by multiplex terminal restriction fragment length polymorphism analysis. Soil under bush had higher pH, C, N, and microbial biomass than under grass, and the microbial community structure was also altered under bush compared to grass. A major disturbance to the ecosystem, bush thinning, resulted in an altered microbial community structure compared to control plots, but the magnitude of this perturbation gradually declined with time. Community structure was primarily driven by pH, C, and N, while vegetation type, bush thinning, and time since bush thinning were of secondary importance.

scholarly journals Microbial Community Analysis of Field-Grown Soybeans with Different Nodulation Phenotypes

2008 ◽  
Vol 74 (18) ◽  
pp. 5704-5709 ◽  
Author(s):  
Seishi Ikeda ◽  
Lynn Esther E. Rallos ◽  
Takashi Okubo ◽  
Shima Eda ◽  
Shoko Inaba ◽  
...  
Keyword(s):  
Principal Component Analysis ◽  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Phylogenetic Analyses ◽  
Principal Component ◽  
Community Analysis ◽  
Component Analysis ◽  
Microbial Community Analysis

ABSTRACT Microorganisms associated with the stems and roots of nonnodulated (Nod−), wild-type nodulated (Nod+), and hypernodulated (Nod++) soybeans [Glycine max (L.) Merril] were analyzed by ribosomal intergenic transcribed spacer analysis (RISA) and automated RISA (ARISA). RISA of stem samples detected no bands specific to the nodulation phenotype, whereas RISA of root samples revealed differential bands for the nodulation phenotypes. Pseudomonas fluorescens was exclusively associated with Nod+ soybean roots. Fusarium solani was stably associated with nodulated (Nod+ and Nod++) roots and less abundant in Nod− soybeans, whereas the abundance of basidiomycetes was just the opposite. The phylogenetic analyses suggested that these basidiomycetous fungi might represent a root-associated group in the Auriculariales. Principal-component analysis of the ARISA results showed that there was no clear relationship between nodulation phenotype and bacterial community structure in the stem. In contrast, both the bacterial and fungal community structures in the roots were related to nodulation phenotype. The principal-component analysis further suggested that bacterial community structure in roots could be classified into three groups according to the nodulation phenotype (Nod−, Nod+, or Nod++). The analysis of root samples indicated that the microbial community in Nod− soybeans was more similar to that in Nod++ soybeans than to that in Nod+ soybeans.

scholarly journals Spatial Variability in Streambed Microbial Community Structure Across Two Watersheds

2021 ◽  
Author(s):  
Philips O. Akinwole ◽  
Jinjun Kan ◽  
Louis A. Kaplan ◽  
Robert H. Findlay
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Biomass ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Water Content ◽  
Microbial Community Structure ◽  
Environmental Heterogeneity ◽  
Sediment Surface ◽  
Total Microbial Biomass

ABSTRACTThe spatial patterns of microbial communities are largely unknown compared to those of macro-fauna and flora. We investigated patterns of microbial community structure on streambed sediments from two watersheds across spatial scales spanning < 1m within a single stream to several hundred km between watersheds. Analyses of phospholipid fatty acids (PLFA) profiles indicated that the variations in microbial community structure were driven by increases in the relative abundance of microeukaryotic photoautotrophs and their contribution to total microbial biomass. Furthermore, streams within watersheds had similar microbial community structure, underscoring within-watershed controls of microbial communities. Moreover, bacterial community structure assayed as either polymerase chain reaction-denaturing gradient gelelectrophoresis (PCR-DGGE) fingerprints or PLFA profiles edited to remove microeukaryotes indicated a distinct watershed-level biogeography. No distinct stream order-level distributions were identified although DGGE analysis clearly indicated that there was greater variability in community structure among 1st-order streams compared to 2nd- and 3rd-order streams into which they flowed. Longitudinal gradients in microbial biomass and structure showed that the greatest variations were associated with 1st order streams within a watershed and 68% of the variation in total microbial biomass was explained by sediment C:N mass ratio, percent Carbon, sediment surface area, and percent water content. This study confirms a distinct microbial biogeography for headwater stream communities driven by environmental heterogeneity across distant watersheds and suggests that eukaryotic photoautotrophs play a key role in structuring sediment microbial communities.IMPORTANCEMicroorganisms in streams drive many biogeochemical reactions of global significance, including nutrient cycling and energy flow, yet the mechanisms responsible for the distribution and composition of streambed microbial communities are not well known. We sampled sediments from multiple streams in two watersheds; Neversink River (New York) and White Clay Creek (Pennsylvania) watersheds and measured microbial biomass, total microbial and bacterial community structures using phospholipid and molecular methods. Microbial and bacterial community structures displayed a distinct watershed-level biogeography. The smallest headwater streams within a watershed showed the greatest variation in microbial biomass, and C:N ratio, percent carbon, sediment surface area and percent water content explained 68% of the variations in microbial biomass. This study indicates a non-random distribution of microbial communities in streambeds, and that microeukaryotic photoautotrophs, environmental heterogeneity and geographical distance influence microbial composition and spatial distribution.

scholarly journals Soil Microbial Community Structure Evolution along Halophyte Succession in Bohai Bay Wetland

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Mingyang Cong ◽  
Di Cao ◽  
Jingkuan Sun ◽  
Fuchen Shi
Keyword(s):  
Community Structure ◽  
Fatty Acid ◽  
Microbial Community ◽  
Microbial Biomass ◽  
Microbial Community Structure ◽  
Phospholipid Fatty Acid ◽  
Structure Evolution ◽  
Bohai Bay ◽  
Wetland Ecosystem ◽  
Soil Microbial Community Structure

It is urgent to recover Bohai Bay costal wetland ecosystem because of covering a large area of severe saline-alkali soil. To explore the relationship between halophyte herbaceous succession and microbial community structure, we chose four local communities which played an important role in improving soil microenvironment. We performed phospholipid fatty acid analysis, measured soil parameters, and evaluated shifts of microbial community structure. Results showed that microbial community structure changed significantly along succession and bacteria community was dominant. Total phospholipid fatty acid content increased in different successional stages but decreased with depth, with similar variations in bacterial and fungal biomass. Soil organic carbon and especially total nitrogen were positively correlated with microbial biomass. Colonization of pioneering salt-tolerant plantsSuaeda glaucain saline-alkali bare land changed total soil microorganism content and composition. These results showed that belowground processes were strongly related with aboveground halophyte succession. Fungal/bacterial ratio, Gram-negative/Gram-positive bacteria ratio, total microbial biomass, and fungi and bacteria content could indicate the degree of succession stages in Bohai Bay wetland ecosystem. And also these findings demonstrated that microbial community biomass and composition evolved along with vegetation succession environmental variables.

scholarly journals Spatial Variability in Streambed Microbial Community Structure across Two Watersheds

2021 ◽  
Author(s):  
Philips O. Akinwole ◽  
Jinjun Kan ◽  
Louis A. Kaplan ◽  
Robert H. Findlay
Keyword(s):  
New York ◽  
Community Structure ◽  
Microbial Community ◽  
Microbial Biomass ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Energy Flow ◽  
Multiple Streams ◽  
White Clay

Microorganisms in streams drive many biogeochemical reactions of global significance, including nutrient cycling and energy flow; yet, the mechanisms responsible for the distribution and composition of streambed microbial communities are not well known. We sampled sediments from multiple streams in two watersheds (Neversink River [New York] and White Clay Creek [WCC; Pennsylvania] watersheds) and measured microbial biomass and total microbial and bacterial community structures using phospholipid and molecular methods.

Sign in / Sign up

Export Citation Format

Share Document