Riparian cottonwood trees and adjacent river sediments have different microbial communities and produce methane with contrasting carbon isotope compositions

2021 ◽  
Author(s):  
Kristian M. Smits ◽  
Daniel S. Grant ◽  
Sara Ellen Johnston ◽  
Matthew J. Bogard ◽  
Stewart B. Rood ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Carbon Isotope ◽  
River Sediments ◽  
Cottonwood Trees

scholarly journals A metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities

2018 ◽  
Author(s):  
Manuel Kleiner ◽  
Xiaoli Dong ◽  
Tjorven Hinzke ◽  
Juliane Wippler ◽  
Erin Thorson ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Carbon Isotope ◽  
Isotope Ratio ◽  
Single Cells ◽  
Stable Carbon Isotope ◽  
Carbon Sources ◽  
Food Sources ◽  
Individual Species ◽  
Stable Carbon

AbstractMeasurements of the carbon stable isotope ratio (δ13C) are widely used in biology to address major questions regarding food sources and metabolic pathways used by organisms. Measurement of these so called stable carbon isotope fingerprints (SIFs) for microbes involved in biogeochemical cycling and microbiota of plants and animals have led to major discoveries in environmental microbiology. Currently, obtaining SIFs for microbial communities is challenging as the available methods either only provide limited taxonomic resolution, such as with the use of lipid biomarkers, or are limited in throughput, such as NanoSIMS imaging of single cells.Here we present “direct Protein-SIF” and the Calis-p software package (https://sourceforge.net/projects/calis-p/), which enable high-throughput measurements of accurate δ13C values for individual species within a microbial community. We benchmark the method using 20 pure culture microorganisms and show that the method reproducibly provides SIF values consistent with gold standard bulk measurements performed with an isotope ratio mass spectrometer. Using mock community samples, we show that SIF values can also be obtained for individual species within a microbial community. Finally, a case study of an obligate bacteria-animal symbiosis showed that direct Protein-SIF confirms previous physiological hypotheses and can provide unexpected new insights into the symbionts’ metabolism. This confirms the usefulness of this new approach to accurately determine δ13C values for different species in microbial community samples.SignificanceTo understand the roles that microorganisms play in diverse environments such as the open ocean and the human intestinal tract, we need an understanding of their metabolism and physiology. A variety of methods such as metagenomics and metaproteomics exist to assess the metabolism of environmental microorganisms based on gene content and gene expression. These methods often only provide indirect evidence for which substrates are used by a microorganism in a community. The direct Protein-SIF method that we developed allows linking microbial species in communities to the environmental carbon sources they consume by determining their stable carbon isotope signature. Direct Protein-SIF also allows assessing which carbon fixation pathway is used by autotrophic microorganisms that directly assimilate CO2.

Assessment of soil microbial communities in surface applied mixtures of Illinois River sediments and biosolids

2007 ◽  
Vol 36 (2-3) ◽  
pp. 176-183 ◽  
Author(s):  
John J. Kelly ◽  
Emmanuel Favila ◽  
Lakhwinder S. Hundal ◽  
John C. Marlin
Keyword(s):  
Microbial Communities ◽  
River Sediments ◽  
Soil Microbial Communities ◽  
Illinois River ◽  
Soil Microbial

scholarly journals Heavy Metal Tolerance Genes Associated With Contaminated Sediments From an E-Waste Recycling River in Southern China

2021 ◽  
Vol 12 ◽  
Author(s):  
Shengqiao Long ◽  
Hui Tong ◽  
Xuxiang Zhang ◽  
Shuyu Jia ◽  
Manjia Chen ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Microbial Community ◽  
Microbial Communities ◽  
Southern China ◽  
Risk Index ◽  
River Sediments ◽  
Microbial Community Composition ◽  
Heavy Metal Tolerance ◽  
Waste Recycling ◽  
The Impact

Heavy metal pollution that results from electronic waste (e-waste) recycling activities has severe ecological environmental toxicity impacts on recycling areas. The distribution of heavy metals and the impact on the bacteria in these areas have received much attention. However, the diversity and composition of the microbial communities and the characteristics of heavy metal resistance genes (HMRGs) in the river sediments after long-term e-waste contamination still remain unclear. In this study, eight river sediment samples along a river in a recycling area were studied for the heavy metal concentration and the microbial community composition. The microbial community consisted of 13 phyla including Firmicutes (ranging from 10.45 to 36.63%), Proteobacteria (11.76 to 32.59%), Actinobacteria (14.81 to 27.45%), and unclassified bacteria. The abundance of Firmicutes increased along with the level of contaminants, while Actinobacteria decreased. A canonical correspondence analysis (CCA) showed that the concentration of mercury was significantly correlated with the microbial community and species distribution, which agreed with an analysis of the potential ecological risk index. Moreover, manually curated HMRGs were established, and the HMRG analysis results according to Illumina high-throughput sequencing showed that the abundance of HMRGs was positively related to the level of contamination, demonstrating a variety of resistance mechanisms to adapt, accommodate, and live under heavy metal-contaminated conditions. These findings increase the understanding of the changes in microbial communities in e-waste recycling areas and extend our knowledge of the HMRGs involved in the recovery of the ecological environment.

scholarly journals Contrasting Effects of Environmental Concentrations of Sulfonamides on Microbial Heterotrophic Activities in Freshwater Sediments

2021 ◽  
Vol 12 ◽  
Author(s):  
Stéphane Pesce ◽  
Laura Kergoat ◽  
Laurianne Paris ◽  
Loren Billet ◽  
Pascale Besse-Hoggan ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Surface Sediments ◽  
Temporal Dynamics ◽  
River Sediments ◽  
Transient Effects ◽  
High Concentration ◽  
Environmental Concentrations ◽  
Natural Stream ◽  
Measured Activity ◽  
Stimulation Of

The sulfonamide antibiotics sulfamethoxazole (SMX) and sulfamethazine (SMZ) are regularly detected in surface sediments of contaminated hydrosystems, with maximum concentrations that can reach tens of μg kg–1 in stream and river sediments. Little is known about the resulting effects on the exposed benthic organisms. Here we investigated the functional response of stream sediment microbial communities exposed for 4 weeks to two levels of environmentally relevant concentrations of SMX and SMZ, tested individually. To this end, we developed a laboratory channel experiment where natural stream sediments were immersed in water contaminated with nominal environmental concentrations of 500 and 5,000 ng L–1 of SMX or SMZ, causing their accumulation in surface sediments. The mean maximum concentrations measured in the sediment (about 2.1 μg SMX kg–1 dw and 4.5 μg SMZ kg–1 dw) were consistent with those reported in contaminated rivers. The resulting chronic exposure had various effects on the functional potential of the sediment microbial communities, according to the substance (SMX or SMZ), the type of treatment (high or low) and the measured activity, with a strong influence of temporal dynamics. Whereas the SMZ treatments resulted in only transient effects on the five microbial activities investigated, we observed a significant stimulation of the β-glucosidase activity over the 28 days in the communities exposed to the high concentration of SMX. Together with the stimulation of aerobic respiration at low SMX concentrations and the reduced concentration observed in the last days, our results suggest a potential biodegradation of sulfonamides by microbial communities from sediments. Given the key functional role of surface sediment microbial communities in streams and rivers, our findings suggest that the frequently reported contamination of sediments by sulfonamides is likely to affect biogeochemical cycles, with possible impact on ecosystem functioning.

scholarly journals Latest Permian carbonate carbon isotope variability traces heterogeneous organic carbon accumulation and authigenic carbonate formation

2017 ◽  
Vol 13 (11) ◽  
pp. 1635-1659 ◽  
Author(s):  
Martin Schobben ◽  
Sebastiaan van de Velde ◽  
Jana Gliwa ◽  
Lucyna Leda ◽  
Dieter Korn ◽  
...  
Keyword(s):  
Organic Carbon ◽  
Microbial Communities ◽  
Carbon Isotope ◽  
Carbonate Rock ◽  
Inorganic Carbon ◽  
Dissolved Inorganic Carbon ◽  
Carbon Accumulation ◽  
Sea Floor ◽  
Carbonate Carbon ◽  
Carbonate Formation

Abstract. Bulk-carbonate carbon isotope ratios are a widely applied proxy for investigating the ancient biogeochemical carbon cycle. Temporal carbon isotope trends serve as a prime stratigraphic tool, with the inherent assumption that bulk micritic carbonate rock is a faithful geochemical recorder of the isotopic composition of seawater dissolved inorganic carbon. However, bulk-carbonate rock is also prone to incorporate diagenetic signals. The aim of the present study is to disentangle primary trends from diagenetic signals in carbon isotope records which traverse the Permian–Triassic boundary in the marine carbonate-bearing sequences of Iran and South China. By pooling newly produced and published carbon isotope data, we confirm that a global first-order trend towards depleted values exists. However, a large amount of scatter is superimposed on this geochemical record. In addition, we observe a temporal trend in the amplitude of this residual δ13C variability, which is reproducible for the two studied regions. We suggest that (sub-)sea-floor microbial communities and their control on calcite nucleation and ambient porewater dissolved inorganic carbon δ13C pose a viable mechanism to induce bulk-rock δ13C variability. Numerical model calculations highlight that early diagenetic carbonate rock stabilization and linked carbon isotope alteration can be controlled by organic matter supply and subsequent microbial remineralization. A major biotic decline among Late Permian bottom-dwelling organisms facilitated a spatial increase in heterogeneous organic carbon accumulation. Combined with low marine sulfate, this resulted in varying degrees of carbon isotope overprinting. A simulated time series suggests that a 50 % increase in the spatial scatter of organic carbon relative to the average, in addition to an imposed increase in the likelihood of sampling cements formed by microbial calcite nucleation to 1 out of 10 samples, is sufficient to induce the observed signal of carbon isotope variability. These findings put constraints on the application of Permian–Triassic carbon isotope chemostratigraphy based on whole-rock samples, which appears less refined than classical biozonation dating schemes. On the other hand, this signal of increased carbon isotope variability concurrent with the largest mass extinction of the Phanerozoic may provide information about local carbon cycling mediated by spatially heterogeneous (sub-)sea-floor microbial communities under suppressed bioturbation.

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