scholarly journals Colonization Habitat Controls Biomass, Composition, and Metabolic Activity of Attached Microbial Communities in the Columbia River Hyporheic Corridor

2017 ◽  
Vol 83 (16) ◽  
Author(s):  
Noah Stern ◽  
Matthew Ginder-Vogel ◽  
James C. Stegen ◽  
Evan Arntzen ◽  
David W. Kennedy ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Organic Carbon ◽  
Microbial Communities ◽  
River Water ◽  
Hyporheic Zone ◽  
Columbia River ◽  
Fluid Source ◽  
Hydrologic Exchange

ABSTRACT Hydrologic exchange plays a critical role in biogeochemical cycling within the hyporheic zone (the interface between river water and groundwater) of riverine ecosystems. Such exchange may set limits on the rates of microbial metabolism and impose deterministic selection on microbial communities that adapt to dynamically changing dissolved organic carbon (DOC) sources. This study examined the response of attached microbial communities (in situ colonized sand packs) from groundwater, hyporheic, and riverbed habitats within the Columbia River hyporheic corridor to “cross-feeding” with either groundwater, river water, or DOC-free artificial fluids. Our working hypothesis was that deterministic selection during in situ colonization would dictate the response to cross-feeding, with communities displaying maximal biomass and respiration when supplied with their native fluid source. In contrast to expectations, the major observation was that the riverbed colonized sand had much higher biomass and respiratory activity, as well as a distinct community structure, compared with those of the hyporheic and groundwater colonized sands. 16S rRNA gene amplicon sequencing revealed a much higher proportion of certain heterotrophic taxa as well as significant numbers of eukaryotic algal chloroplasts in the riverbed colonized sand. Significant quantities of DOC were released from riverbed sediment and colonized sand, and separate experiments showed that the released DOC stimulated respiration in the groundwater and piezometer colonized sand. These results suggest that the accumulation and degradation of labile particulate organic carbon (POC) within the riverbed are likely to release DOC, which may enter the hyporheic corridor during hydrologic exchange, thereby stimulating microbial activity and imposing deterministic selective pressure on the microbial community composition. IMPORTANCE The influence of river water-groundwater mixing on hyporheic zone microbial community structure and function is an important but poorly understood component of riverine biogeochemistry. This study employed an experimental approach to gain insight into how such mixing might be expected to influence the biomass, respiration, and composition of hyporheic zone microbial communities. Colonized sands from three different habitats (groundwater, river water, and hyporheic) were “cross-fed” with either groundwater, river water, or DOC-free artificial fluids. We expected that the colonization history would dictate the response to cross-feeding, with communities displaying maximal biomass and respiration when supplied with their native fluid source. By contrast, the major observation was that the riverbed communities had much higher biomass and respiration, as well as a distinct community structure compared with those of the hyporheic and groundwater colonized sands. These results highlight the importance of riverbed microbial metabolism in organic carbon processing in hyporheic corridors.

scholarly journals Effects of Thinning on Microbial Community Structure in the Organic Horizon of Chinese Pine Plantations in Badaling, Beijing, China

Forests ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 828 ◽  
Author(s):  
Wang ◽  
Zhao ◽  
Sun ◽  
Yang ◽  
Zhou
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Organic Carbon ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Pine Plantations ◽  
Pinus Tabulaeformis ◽  
Organic Horizon ◽  
Moderate Intensity ◽  
Chinese Pine

Research Highlights: Moderate thinning can effectively improve forestry production and change the microenvironment of understory vegetation. Background and Objectives: Microbial communities control the decomposition and transformation of forest organic matter; however, the influence of thinning on microbes in the organic horizon remains unclear. Materials and Methods: In this study, we subjected four plots of Chinese pine plantations in Badaling, Beijing to different thinning intensities, including no thinning (T0), low-intensity thinning (T10), medium-intensity thinning (T20), and high-intensity thinning (T50). The changes in chemical properties and microbial community compositions observed in the organic horizon, which comprised undecomposed litter (L layer) and half-decomposed litter (F layer), were analyzed after thinning. Microbial community compositions were evaluated using phospholipid fatty acid (PLFA) methods. Results: The results showed that the abundances of gram-negative bacteria (GN) and total bacteria (B) under the T10 thinning condition were the highest among the four thinning intensities, and the abundance of arbuscular mycorrhizal fungi (AMF) in T20 was higher than under other thinning intensities. The abundance of gram-positive bacteria (GP) and actinobacteria (ACT) in T10 was lower than in both T0 and T50. The abundance of total PLFAs and fungi (FU) was higher in the L layer, whereas the abundance of GP, GN, B, ACT, and AMF was higher in the F layer. Conclusions: Our results demonstrated that the L layer better reflects the influence of thinning on litter. Redundancy analysis (RDA) results indicated that the organic carbon (LOC) , dissolved organic carbon (DOC), and ammonium nitrogen (NH4+-N)contents of litter were primarily responsible for the observed changes in microbial community structure, with LOC alone explaining 62.6% of the total variance among the litter substrate factors selected. Overall, moderate-intensity thinning of Pinus tabulaeformis Carr. plantations created more favorable conditions for microbial communities in the organic horizon.

scholarly journals Seasonal Dynamics of Shallow-Hyporheic-Zone Microbial Community Structure along a Heavy-Metal Contamination Gradient

2004 ◽  
Vol 70 (4) ◽  
pp. 2323-2331 ◽  
Author(s):  
Kevin P. Feris ◽  
Philip W. Ramsey ◽  
Chris Frazar ◽  
Matthias Rillig ◽  
Johnnie N. Moore ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Metal Contamination ◽  
Hyporheic Zone ◽  
Heavy Metal Contamination ◽  
The Difference

ABSTRACT Heavy metals contaminate numerous freshwater streams and rivers worldwide. Previous work by this group demonstrated a relationship between the structure of hyporheic microbial communities and the fluvial deposition of heavy metals along a contamination gradient during the fall season. Seasonal variation has been documented in microbial communities in numerous terrestrial and aquatic environments, including the hyporheic zone. The current study was designed to assess whether relationships between hyporheic microbial community structure and heavy-metal contamination vary seasonally by monitoring community structure along a heavy-metal contamination gradient for more than a year. No relationship between total bacterial abundance and heavy metals was observed (R 2 = 0.02, P = 0.83). However, denaturing gradient gel electrophoresis pattern analysis indicated a strong and consistent linear relationship between the difference in microbial community composition (populations present) and the difference in the heavy metal content of hyporheic sediments throughout the year (R 2 = 0.58, P < 0.001). Correlations between heavy-metal contamination and the abundance of four specific phylogenetic groups (most closely related to the α, β, and γ-proteobacteria and cyanobacteria) were apparent only during the fall and early winter, when the majority of organic matter is deposited into regional streams. These seasonal data suggest that the abundance of susceptible populations responds to heavy metals primarily during seasons when the potential for growth is highest.

scholarly journals Differences in Hyporheic-Zone Microbial Community Structure along a Heavy-Metal Contamination Gradient

2003 ◽  
Vol 69 (9) ◽  
pp. 5563-5573 ◽  
Author(s):  
Kevin Feris ◽  
Philip Ramsey ◽  
Chris Frazar ◽  
Johnnie N. Moore ◽  
James E. Gannon ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Metal Contamination ◽  
Metal Content ◽  
Hyporheic Zone ◽  
Heavy Metal Contamination ◽  
Sediment Metal

ABSTRACT The hyporheic zone of a river is nonphotic, has steep chemical and redox gradients, and has a heterotrophic food web based on the consumption of organic carbon entrained from downwelling surface water or from upwelling groundwater. The microbial communities in the hyporheic zone are an important component of these heterotrophic food webs and perform essential functions in lotic ecosystems. Using a suite of methods (denaturing gradient gel electrophoresis, 16S rRNA phylogeny, phospholipid fatty acid analysis, direct microscopic enumeration, and quantitative PCR), we compared the microbial communities inhabiting the hyporheic zone of six different river sites that encompass a wide range of sediment metal loads resulting from large base-metal mining activity in the region. There was no correlation between sediment metal content and the total hyporheic microbial biomass present within each site. However, microbial community structure showed a significant linear relationship with the sediment metal loads. The abundances of four phylogenetic groups (groups I, II, III, and IV) most closely related to α-, β-, and γ-proteobacteria and the cyanobacteria, respectively, were determined. The sediment metal content gradient was positively correlated with group III abundance and negatively correlated with group II abundance. No correlation was apparent with regard to group I or IV abundance. This is the first documentation of a relationship between fluvially deposited heavy-metal contamination and hyporheic microbial community structure. The information presented here may be useful in predicting long-term effects of heavy-metal contamination in streams and provides a basis for further studies of metal effects on hyporheic microbial communities.

scholarly journals Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities

mSystems ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Manuel Kleiner
Keyword(s):  
Gene Expression ◽  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Large Scale ◽  
Molecular Level ◽  
Carbon Sources ◽  
Community Members ◽  
Insight Into

ABSTRACT Metaproteomics is the large-scale identification and quantification of proteins from microbial communities and thus provides direct insight into the phenotypes of microorganisms on the molecular level. Initially, metaproteomics was mainly used to assess the “expressed” metabolism and physiology of microbial community members. However, recently developed metaproteomic tools allow quantification of per-species biomass to determine community structure, in situ carbon sources of community members, and the uptake of labeled substrates by community members. In this perspective, I provide a brief overview of the questions that we can currently address, as well as new metaproteomics-based approaches that we and others are developing to address even more questions in the study of microbial communities and plant and animal microbiota. I also highlight some areas and technologies where I anticipate developments and potentially major breakthroughs in the next 5 years and beyond.

Phylum-Specific Primer Design and Implication in Quantification of the Microbial Community Structure in GuJingGong Pit Mud

2014 ◽  
Vol 1051 ◽  
pp. 311-316 ◽  
Author(s):  
Xi Mei Luo ◽  
Zhi Lei Gao ◽  
Hui Min Zhang ◽  
An Jun Li ◽  
Hong Kui He ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Real Time Quantitative Pcr ◽  
Sequencing Technologies ◽  
Specific Pcr ◽  
Pit Mud ◽  
Almost All ◽  
Polymerase Chain Reaction Primers

In recent years, despite the significant improvement of sequencing technologies such as the pyrosequencing, rapid evaluation of microbial community structures remains very difficult because of the abundance and complexity of organisms in almost all natural microbial communities. In this paper, a group of phylum-specific primers were elaborately designed based on a single nucleotide discrimination technology to quantify the main microbial community structure from GuJingGong pit mud samples using the real-time quantitative PCR (qPCR). Specific PCR (polymerase chain reaction) primers targeting a particular group would provide promising sensitivity and more in-depth assessment of microbial communities.

scholarly journals High-throughput amplicon sequencing reveals the spatiotemporal effects, abiotic and biotic shaping factors for the microbial communities in tropical mangrove sediments in Sanya, China

2020 ◽  
Author(s):  
Wu Qu ◽  
Boliang Gao ◽  
Jie Wu ◽  
Min Jin ◽  
Jianxin Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Fungal Community ◽  
Amplicon Sequencing ◽  
Biotic Factors ◽  
Community Structures ◽  
Mangrove Sediments ◽  
Element Cycling ◽  
Microbial Community Structures

Abstract Background Microbial roles in element cycling and nutrient providing are crucial for mangrove ecosystems and serve as important regulators for climate change in Earth ecosystem. However, some key information about the spatiotemporal influences and abiotic and biotic shaping factors for the microbial communities in mangrove sediments remains lacking. Methods In this work, 22 sediment samples were collected from multiple spatiotemporal dimensions, including three locations, two depths, and four seasons, and the bacterial, archaeal, and fungal community structures in these samples were studied using amplicon sequencing. Results The microbial community structures were varied in the samples from different depths and locations based on the results of LDA effect size analysis, principal coordinate analysis, the analysis of similarities, and permutational multivariate ANOVA. However, these microbial community structures were stable among the seasonal samples. Linear fitting models and Mantel test showed that among the 13 environmental factors measured in this study, the sediment particle size (PS) was the key abiotic shaping factor for the bacterial, archaeal, or fungal community structure. Besides PS, salinity and humidity were also significant impact factors according to the canonical correlation analysis (p ≤ 0.05). Co-occurrence networks demonstrated that the bacteria assigned into phyla Ignavibacteriae, Proteobacteria, Bacteroidetes, Chloroflexi, and Acidobacteria were the key biotic factors for shaping the bacterial community in mangrove sediments. Conclusions This work showed the variability on spatial dimensions and the stability on temporal dimension for the bacterial, archaeal, or fungal microbial community structure, indicating that the tropical mangrove sediments are versatile but stable environments. PS served as the key abiotic factor could indirectly participate in material circulation in mangroves by influencing microbial community structures, along with salinity and humidity. The bacteria as key biotic factors were found with the abilities of photosynthesis, polysaccharide degradation, or nitrogen fixation, which were potential indicators for monitoring mangrove health, as well as crucial participants in the storage of mangrove blue carbons and mitigation of climate warming. This study expanded the knowledge of mangroves for the spatiotemporal variation, distribution, and regulation of the microbial community structures, thus further elucidating the microbial roles in mangrove management and climate regulation.

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