Partitioning of bacterial communities between travertine depositional facies at Mammoth Hot Springs, Yellowstone National Park, U.S.A.

2003 ◽  
Vol 40 (11) ◽  
pp. 1531-1548 ◽  
Author(s):  
Bruce W Fouke ◽  
George T Bonheyo ◽  
Beth Sanzenbacher ◽  
Jorge Frias-Lopez
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Communities ◽  
Yellowstone National Park ◽  
National Park ◽  
Hot Springs ◽  
Bacterial Community Composition ◽  
Drainage System ◽  
Rrna Genes ◽  
Depositional Facies

A culture-independent molecular survey indicates that the composition of bacterial communities is distinctly partitioned between travertine depositional facies in the surface drainage system of Spring AT-1 at Angel Terrace, Mammoth Hot Springs, Yellowstone National Park. PCR (polymerase chain reaction) amplification and sequencing of 16S rRNA genes with universally conserved bacterial primers has identified over 553 unique partial and 104 complete gene sequences (derived from more than 14 000 clones), affiliated with 221 unique species that represent 21 bacterial divisions. These sequences exhibited < 12% similarity in bacterial community composition between each of the travertine depositional facies. This implies that relatively little downstream bacterial transport and colonization took place despite the rapid and continuous flow of spring water from the high-temperature to low-temperature facies. These results suggest that travertine depositional facies, which are independently determined by the physical and chemical conditions of the hot spring drainage system, effectively predict bacterial community composition as well as the morphology and chemistry of travertine precipitation.

scholarly journals Links between Plant and Rhizoplane Bacterial Communities in Grassland Soils, Characterized Using Molecular Techniques

2005 ◽  
Vol 71 (11) ◽  
pp. 6784-6792 ◽  
Author(s):  
Naoise Nunan ◽  
Timothy J. Daniell ◽  
Brajesh K. Singh ◽  
Artemis Papert ◽  
James W. McNicol ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Plant Species ◽  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Bacterial Community Composition ◽  
Molecular Techniques ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Grassland Soils

ABSTRACT Molecular analysis of grassland rhizosphere soil has demonstrated complex and diverse bacterial communities, with resultant difficulties in detecting links between plant and bacterial communities. These studies have, however, analyzed “bulk” rhizosphere soil, rather than rhizoplane communities, which interact most closely with plants through utilization of root exudates. The aim of this study was to test the hypothesis that plant species was a major driver for bacterial rhizoplane community composition on individual plant roots. DNA extracted from individual roots was used to determine plant identity, by analysis of the plastid tRNA leucine (trnL) UAA gene intron, and plant-related bacterial communities. Bacterial communities were characterized by analysis of PCR-amplified 16S rRNA genes using two fingerprinting methods: terminal restriction fragment length polymorphisms (T-RFLP) and denaturing gradient gel electrophoresis (DGGE). Links between plant and bacterial rhizoplane communities could not be detected by visual examination of T-RFLP patterns or DGGE banding profiles. Statistical analysis of fingerprint patterns did not reveal a relationship between bacterial community composition and plant species but did demonstrate an influence of plant community composition. The data also indicated that topography and other, uncharacterized, environmental factors are important in driving bacterial community composition in grassland soils. T-RFLP had greater potential resolving power than DGGE, but findings from the two methods were not significantly different.

scholarly journals Isolation, Characterization, and Ecology of Sulfur-Respiring Crenarchaea Inhabiting Acid-Sulfate-Chloride-Containing Geothermal Springs in Yellowstone National Park

2007 ◽  
Vol 73 (20) ◽  
pp. 6669-6677 ◽  
Author(s):  
Eric S. Boyd ◽  
Robert A. Jackson ◽  
Gem Encarnacion ◽  
James A. Zahn ◽  
Trevor Beard ◽  
...  
Keyword(s):  
Yellowstone National Park ◽  
National Park ◽  
Hot Springs ◽  
Lipid Fraction ◽  
Carbon Sources ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Pcr Analysis ◽  
Geothermal Springs ◽  
Physiological Characterization

ABSTRACT Elemental sulfur (S0) is associated with many geochemically diverse hot springs, yet little is known about the phylogeny, physiology, and ecology of the organisms involved in its cycling. Here we report the isolation, characterization, and ecology of two novel, S0-reducing Crenarchaea from an acid geothermal spring referred to as Dragon Spring. Isolate 18U65 grows optimally at 70 to 72°C and at pH 2.5 to 3.0, while isolate 18D70 grows optimally at 81°C and pH 3.0. Both isolates are chemoorganotrophs, dependent on complex peptide-containing carbon sources, S0, and anaerobic conditions for respiration-dependent growth. Glycerol dialkyl glycerol tetraethers (GDGTs) containing four to six cyclopentyl rings were present in the lipid fraction of isolates 18U65 and 18D70. Physiological characterization suggests that the isolates are adapted to the physicochemical conditions of Dragon Spring and can utilize the natural organic matter in the spring as a carbon and energy source. Quantitative PCR analysis of 16S rRNA genes associated with the S0 flocs recovered from several acid geothermal springs using isolate-specific primers indicates that these two populations together represent 17 to 37% of the floc-associated DNA. The physiological characteristics of isolates 18U65 and 18D70 are consistent with their potential widespread distribution and putative role in the cycling of sulfur in acid geothermal springs throughout the Yellowstone National Park geothermal complex. Based on phenotypic and genetic characterization, the designations Caldisphaera draconis sp. nov. and Acidilobus sulfurireducens sp. nov. are proposed for isolates 18U65 and 18D70, respectively.

scholarly journals Rhizobacterial communities of five co-occurring desert halophytes

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5508 ◽  
Author(s):  
Yan Li ◽  
Yan Kong ◽  
Dexiong Teng ◽  
Xueni Zhang ◽  
Xuemin He ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Plant Species ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Community Diversity ◽  
Species Identity ◽  
Halostachys Caspica ◽  
Lycium Ruthenicum ◽  
Limonium Gmelinii

BackgroundRecently, researches have begun to investigate the microbial communities associated with halophytes. Both rhizobacterial community composition and the environmental drivers of community assembly have been addressed. However, few studies have explored the structure of rhizobacterial communities associated with halophytic plants that are co-occurring in arid, salinized areas.MethodsFive halophytes were selected for study: these co-occurred in saline soils in the Ebinur Lake Nature Reserve, located at the western margin of the Gurbantunggut Desert of Northwestern China. Halophyte-associated bacterial communities were sampled, and the bacterial 16S rDNA V3–V4 region amplified and sequenced using the Illumina Miseq platform. The bacterial community diversity and structure were compared between the rhizosphere and bulk soils, as well as among the rhizosphere samples. The effects of plant species identity and soil properties on the bacterial communities were also analyzed.ResultsSignificant differences were observed between the rhizosphere and bulk soil bacterial communities. Diversity was higher in the rhizosphere than in the bulk soils. Abundant taxonomic groups (from phylum to genus) in the rhizosphere were much more diverse than in bulk soils. Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Planctomycetes were the most abundant phyla in the rhizosphere, while Proteobacteria and Firmicutes were common in bulk soils. Overall, the bacterial community composition were not significantly differentiated between the bulk soils of the five plants, but community diversity and structure differed significantly in the rhizosphere. The diversity ofHalostachys caspica,Halocnemum strobilaceumandKalidium foliatumassociated bacterial communities was lower than that ofLimonium gmeliniiandLycium ruthenicumcommunities. Furthermore, the composition of the bacterial communities ofHalostachys caspicaandHalocnemum strobilaceumwas very different from those ofLimonium gmeliniiandLycium ruthenicum. The diversity and community structure were influenced by soil EC, pH and nutrient content (TOC, SOM, TON and AP); of these, the effects of EC on bacterial community composition were less important than those of soil nutrients.DiscussionHalophytic plant species played an important role in shaping associated rhizosphere bacterial communities. When salinity levels were constant, soil nutrients emerged as key factors structuring bacterial communities, while EC played only a minor role. Pairwise differences among the rhizobacterial communities associated with different plant species were not significant, despite some evidence of differentiation. Further studies involving more halophyte species, and individuals per species, are necessary to elucidate plant species identity effects on the rhizosphere for co-occurring halophytes.

Potential Oxygen Consumption and Community Composition of Sediment Bacteria in a Seasonally Hypoxic Enclosed Bay

2021 ◽  
Author(s):  
Fumiaki Mori ◽  
Yu Umezawa ◽  
Ruji Kondo ◽  
Gregory N. Nishihara ◽  
Minoru Wada
Keyword(s):  
Oxygen Consumption ◽  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sediment Surface ◽  
Tetrazolium Chloride ◽  
Sediment Samples ◽  
Potential Oxygen

Abstract The dynamics of potential oxygen consumption at the sediment surface in a seasonally hypoxic bay were monitored monthly by applying a tetrazolium dye (2-(4-iodophenyl)-3-(4-nitrophenyl)-5-phenyl-2H-tetrazolium chloride [INT]) reduction assay to intact sediment core samples for two consecutive years (2012–2013). Based on the empirically determined correlation between INT reduction (INT-formazan formation) and actual oxygen consumption of sediment samples, we inferred the relative contribution of biological and non-biological (chemical) processes to the potential whole oxygen consumption in the collected sediment samples. It was demonstrated that both potentials consistently increased and reached a maximum during summer hypoxia in each year. For samples collected in 2012, amplicon sequence variants (ASVs) of the bacterial 16S rRNA genes derived from the sediment surface revealed a notable shift in the bacterial community composition before and after the INT assay incubation. Within the bacterial community that was predominated by the ASVs closely related to Woeseia (Woeseiaceae, Gammaproteobacteria), the relative abundance of ASVs affiliated with Arcobacter (Arcobacteraceae, Campylobacteria), a putative sulfur-oxidizing bacterial genus, increased markedly in the summer samples. These findings have implications not only for the group of bacteria that are consistently responsible for the consumption of dissolved oxygen (DO) year-round in the sediment, but also for those that might grow rapidly in response to episodic DO supply on the sediment surface during midst of seasonal hypoxia.

scholarly journals Significant Differences in the Gut Bacterial Communities of Hooded Crane (Grus monacha) in Different Seasons at a Stopover Site on the Flyway

Animals ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 701 ◽  
Author(s):  
Fengling Zhang ◽  
Xingjia Xiang ◽  
Yuanqiu Dong ◽  
Shaofei Yan ◽  
Yunwei Song ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Bacterial Community Composition ◽  
Stopover Site ◽  
Intestinal Bacterial Community ◽  
Hooded Crane ◽  
Grus Monacha

Intestinal bacterial communities form an integral component of the organism. Many factors influence gut bacterial community composition and diversity, including diet, environment and seasonality. During seasonal migration, birds use many habitats and food resources, which may influence their intestinal bacterial community structure. Hooded crane (Grus monacha) is a migrant waterbird that traverses long distances and occupies varied habitats. In this study, we investigated the diversity and differences in intestinal bacterial communities of hooded cranes over the migratory seasons. Fecal samples from hooded cranes were collected at a stopover site in two seasons (spring and fall) in Lindian, China, and at a wintering ground in Shengjin Lake, China. We analyzed bacterial communities from the fecal samples using high throughput sequencing (Illumina Mi-seq). Firmicutes, Proteobacteria, Tenericutes, Cyanobacteria, and Actinobacteria were the dominant phyla across all samples. The intestinal bacterial alpha-diversity of hooded cranes in winter was significantly higher than in fall and spring. The bacterial community composition significantly differed across the three seasons (ANOSIM, P = 0.001), suggesting that seasonal fluctuations may regulate the gut bacterial community composition of migratory birds. This study provides baseline information on the seasonal dynamics of intestinal bacterial community structure in migratory hooded cranes.

scholarly journals Multiple Stressors Determine Community Structure and Estimated Function of River Biofilm Bacteria

2020 ◽  
Vol 86 (12) ◽  
Author(s):  
Ferran Romero ◽  
Vicenç Acuña ◽  
Sergi Sabater
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Communities ◽  
Pesticide Exposure ◽  
Multiple Stressors ◽  
Bacterial Community Composition ◽  
Freshwater Ecosystems ◽  
Low Flow ◽  
Hydrological Stress ◽  
The Individual

ABSTRACT Freshwater ecosystems are exposed to multiple stressors, but their individual and combined effects remain largely unexplored. Here, we investigated the response of stream biofilm bacterial communities to warming, hydrological stress, and pesticide exposure. We used 24 artificial streams on which epilithic (growing on coarse sediments) and epipsammic (growing on fine sediments) stream biofilms were maintained. Bacterial community composition and estimated function of biofilms exposed during 30 days to individual and combined stressors were assessed using 16S rRNA gene metabarcoding. Among the individual effects by stressors, hydrological stress (i.e., a simulated low-flow situation) was the most relevant, since it significantly altered 57% of the most abundant bacterial taxa (n = 28), followed by warming (21%) and pesticide exposure (11%). Regarding the combined effects, 16% of all stressor combinations resulted in significant interactions on bacterial community composition and estimated function. Antagonistic responses prevailed (57 to 89% of all significant interactions), followed by synergisms (11 to 43%), on specific bacterial taxa, indicating that multiple-stressor scenarios could lead to unexpected shifts in the community composition and associated functions of riverine bacterial communities. IMPORTANCE Freshwater ecosystems such as rivers are of crucial importance for human well-being. However, human activities result in many stressors (e.g., toxic chemicals, increased water temperatures, and hydrological alterations) cooccurring in rivers and streams worldwide. Among the many organisms inhabiting rivers and streams, bacteria are ecologically crucial; they are placed at the base of virtually all food webs and they recycle the organic matter needed for bigger organisms. Most of these bacteria are in close contact with river substratum, where they form the biofilms. There is an urgent need to evaluate the effects of these stressors on river biofilms, so we can anticipate future environmental problems. In this study, we experimentally exposed river biofilms to a pesticide mixture, an increase in water temperature and a simulated low-flow condition, in order to evaluate the individual and joint effects of these stressors on the bacterial community composition and estimated function.

Variation of bacterial communities in Muztagh ice core from 1869 to 2000

2020 ◽  
Author(s):  
Yongqin Liu ◽  
Tandong Yao ◽  
Baiqing Xu
Keyword(s):  
Bacterial Community ◽  
Temporal Variation ◽  
Community Composition ◽  
Bacterial Communities ◽  
Environmental Variables ◽  
Climate Changes ◽  
Bacterial Community Composition ◽  
Ice Core ◽  
The Past ◽  
Stage 1

&lt;p&gt;Many studies focusing on the physical and chemical indicators of the ice core reflected the climate changes. However, only few biological indicators indicated the past climate changes which are mainly focused in biomass rather than diversity. How the biodiversity response to the climate change during the past hundred years is still unknow. Glaciers in Mt. Muztagh Ata region are in&amp;#64258;uenced by the year-round westerly circulation. We firstly disclosed annual variations of bacterial community compositions in ice core over the past 130 years from Muztagh Glacier, the western Tibetan Plateau. Temporal variation in bacterial abundance was strongly controlled by DOC, TN, &amp;#948;&lt;sup&gt;18&lt;/sup&gt;O, Ca&lt;sup&gt;2+&lt;/sup&gt;, SO&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;2&lt;/sup&gt;&lt;sup&gt;&amp;#8722;&lt;/sup&gt;, NH&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;+&lt;/sup&gt; and NO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;&amp;#8722;&lt;/sup&gt;. Proteobacteria, Actinobacteria and Firmicutes were the three most abundant bacterial phyla, accounting for 49.3%, 21.3% and 11.0% of the total community, respectively. The abundances of Firmicutes and Bacteroidetes pronouncedly increased over time throughout the entire ice core. UPGMA cluster analysis of the bacterial community composition separated the all ice core samples into two main clusters along the temporal variation. The first cluster consisted of samples from 1951 to 2000 and the second cluster contained main samples during the period of 1869-1950. The stage 1 and stage 2 bacterial community dissimilarities increased linearly with time on the basis of the Bray-Curtis distance, indicating a similar temporal&amp;#8211;decay relationship between the stage 1 and stage 2 bacterial communities. Of all the environmental variables examined, only DOC and NH&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;+&lt;/sup&gt; exhibited very strong negative correlations with bacterial Chao1-richness. &lt;sup&gt;18&lt;/sup&gt;O was another important variable in shaping the ice core bacterial community composition and contributed 1.6% of the total variation. Moreover, DistLM analysis indicated that the environmental variables explained more variation in the stage 1 community (20.1%) than that of the stage 2 community (19.9%).&lt;/p&gt;

scholarly journals Composition and stability of bacterial communities associated with granular activated carbon and anthracite filters in a pilot scale municipal drinking water treatment facility

2012 ◽  
Vol 10 (2) ◽  
pp. 244-255 ◽  
Author(s):  
T. B. Shirey ◽  
R. W. Thacker ◽  
J. B. Olson
Keyword(s):  
Drinking Water ◽  
Activated Carbon ◽  
Community Structure ◽  
Water Treatment ◽  
Bacterial Community ◽  
16S Rrna ◽  
Community Composition ◽  
Bacterial Communities ◽  
Granular Activated Carbon ◽  
Rrna Genes

Granular activated carbon (GAC) is an alternative filter substrate for municipal water treatment as it provides a high surface area suitable for microbial colonization. The resulting microbial growth promotes biodegradation of organic materials and other contaminants from influent waters. Here, the community structure of the bacteria associated with three GAC and two anthracite filters was examined over 12 months to monitor changes in community composition. Nearly complete 16S rRNA genes were polymerase chain reaction amplified for terminal restriction fragment length polymorphism (T-RFLP) analyses. The identity of commonly occurring peaks was determined through the construction of five representative 16S rRNA clone libraries. Based on sequence analysis, the bacterial communities associated with both anthracite and GAC filters appear to be composed of environmentally derived bacteria, with no known human pathogens. Analysis of similarity tests revealed that significant differences in bacterial community structure occurred over time, with filter substrate playing an important role in determining community composition. GAC filters exhibited the greatest degree of bacterial community variability over the sampling period, while anthracite filters showed a lower degree of variability and less change in community composition. Thus, GAC may be a suitable biologically active filter substrate for the treatment of municipal drinking water.

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