A hydrocarbon-contaminated aquifer reveals a Piggyback-the-Persistent viral strategy

2019 ◽  
Vol 95 (8) ◽  
Author(s):  
James S Paterson ◽  
Renee J Smith ◽  
Jody C McKerral ◽  
Lisa M Dann ◽  
Elise Launer ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Carbon Sources ◽  
Relative Importance ◽  
Contaminated Aquifer ◽  
Nutrient Sources ◽  
Microbial Process ◽  
Subsurface Environments ◽  
The Common

ABSTRACT Subsurface environments hold the largest reservoir of microbes in the biosphere. They play essential roles in transforming nutrients, degrading contaminants and recycling organic matter. Here, we propose a previously unrecognised fundamental microbial process that influences aquifer bioremediation dynamics and that applies to all microbial communities. In contrast to previous models, our proposed Piggyback-the-Persistent (PtP) mechanism occurs when viruses become more dominated by those exhibiting temperate rather than lytic lifestyles driven by persistent chemicals (in our case chlorinated-hydrocarbon pollutants) that provide long-term carbon sources and that refocus the aquifer carbon cycle, thus altering the microbial community. In this ultra-oligotrophic system, the virus:microbial ratio (VMR) ranges from below the detection limit of 0.0001 to 0.6, well below the common aquatic range of 3–10. Shortest-average-path network analysis revealed VMR and trichlorethene (TCE) as nodes through which ecosystem information and biomass most efficiently pass. Novel network rearrangement revealed a hierarchy of Kill-the-Winner (KtW), Piggyback-the-Winner (PtW) and PtP nodes. We propose that KtW, PtW and PtP occur simultaneously as competing strategies, with their relative importance depending on conditions at a particular time and location with unusual nutrient sources, such as TCE, appearing to contribute to a shift in this balance between viral mechanisms.

Soil bacterial communities interact with silicon fraction transformation and promote rice yield after long-term straw return

2021 ◽  
Author(s):  
Alin Song ◽  
Zimin Li ◽  
Fenliang Fan
Keyword(s):  
Microbial Community ◽  
Rice Yield ◽  
Soil Microbial Communities ◽  
Nutrient Sources ◽  
Soil Microbial ◽  
Mn Oxide ◽  
Straw Return ◽  
Soil Bacterial ◽  
Healthy Growth

<p>Returning crop straw into soil is an important practice to balance biogenic and bioavailable silicon (Si) pool in paddy, which is crucial for rice healthy growth. However, it remains elusive how straw return affects Si bioavailability, its uptake, and rice yield, owing to little knowledge about soil microbial communities responsible for straw degradation. Here, we investigated the change of soil Si fractions and microbial community in a 39-year-old paddy field amended by a long-term straw return. Results showed that rice straw-return significantly increased soil bioavailable Si and rice yield to from 29.9% to 61.6% and from 14.5% to 23.6%, respectively, compared to NPK fertilization alone. Straw return significantly altered soil microbial community abundance. Acidobacteria was positively and significantly related to amorphous Si, while Rokubacteria at the phylum level, Deltaproteobacteria and Holophagae at the class level were negatively and significantly related to organic matter adsorbed and Fe/Mn-oxide combined Si in soils. Redundancy analysis of their correlations further demonstrated that Si status significantly explained 12% of soil bacterial community variation. These findings suggest that soil bacteria community and diversity interact with Si mobility via altering its transformation, resulting in the balance of various nutrient sources to drive biological silicon cycle in agroecosystem.</p>

Organic matter additions to soil and effects on microbially mediated carbon cycling

2020 ◽  
Author(s):  
Rachel hasler ◽  
Mark pawlett ◽  
Jim harris ◽  
Helen bostock ◽  
Marc redmile-gordon
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Carbon Cycling ◽  
Community Composition ◽  
Soil Microbial Community ◽  
Microbial Community Composition ◽  
Soil Microbial ◽  
Horse Manure ◽  
Soil Microbial Community Composition

<p>The type of soil organic amendment selected can have profound implications for carbon cycling processes in soils. Understanding the link between this choice and its effect on the soil microbiome will improve our understanding of the capacity of these materials to improve carbon sequestration and cycling dynamics. Understanding and facilitating the lifestyle strategies of microorganisms processing organic matter is essential to improving our understanding of the terrestrial carbon cycle. This research focuses on utilising organic amendments to alter the indigenous soil microbial community composition and function to improve the capacity of the soil to cycle and store carbon in horticultural soils.  The effects of annual application of various organic fertilisers (peat, bracken, bark, horse manure, garden compost) in a long-term (10year) field experiment were explored. Sampling was completed pre and post application of organic matter within one season (following 10 years of applications) to identify which organic amendment was more effective in producing benefits to plants through improved soil organic matter and which amendments provide the greatest legacy effect on carbon cycling. The response of the soil microbial community composition (phospholipid fatty acid analysis) and carbon functional cycling dynamics (respiration using MicroResp™) were determined with a view to improving our understanding of the interaction between the materials applied and microbial processes. PCA of the MicroResp™ data identified that all treatments had a different functional profile compared to the control[PM1]  with peat being significantly different from all other treatments. Horse manure and bark differed significantly within a single growing season; prior and post organic matter addition in spring 2019.  Microbial biomass measurements for garden compost and horse manure were significantly higher following organic matter addition compared to all other treatments and the control[PM2] .  All treatments had a significant effect [PM3] on hot water extractable carbon and total carbon. Peat had a significantly different effect[PM4] , when compared to other treatments, on the soil PLFA profile and bark application significantly increased [PM5] the neutral lipid (NLFA) biomarker 16:1ω5.  Bark and horse manure application both significantly increased PLFA fungal biomarker 18:2ω6,9. No significant differences were found between the fungal/bacterial ratios of the organic matter additions prior to being added to the soil. These findings show that altering the resources available to the soil microbial community has a significant impact on soil microbial community composition and microbially mediated carbon cycling functionality. Increasing our understanding of how soil functions are altered by land management decisions will enable better informed predictions of the long-term benefits of organic matter applications on carbon sequestration and cycling dynamics.</p>

scholarly journals Large herbivorous wildlife and livestock differentially influence the relative importance of different sources of carbon for riverine food webs

2021 ◽  
Author(s):  
Frank O. Masese ◽  
Thomas Fuss ◽  
Lukas Bistarelli ◽  
Caroline Buchen-Tschiskale ◽  
Gabriel Singer
Keyword(s):  
Organic Matter ◽  
Food Webs ◽  
Aquatic Ecosystems ◽  
Carbon Sources ◽  
Large River ◽  
Livestock Grazing ◽  
Relative Importance ◽  
River Continuum ◽  
Aquatic Food ◽  
Different Sources

In many regions around the world, large populations of native wildlife have declined or been replaced by livestock grazing areas and farmlands, with consequences on terrestrial-aquatic ecosystems connectivity and trophic resources supporting food webs in aquatic ecosystems. The river continuum concept (RCC) and the riverine productivity model (RPM) predict a shift of carbon supplying aquatic food webs along the river: from terrestrial inputs in low-order streams to autochthonous production in mid-sized rivers. Here, we studied the influence of replacing large wildlife (mainly hippos) with livestock on the relative importance of C3 vegetation, C4 grasses and periphyton on macroinvertebrates in the Mara River, which is an African montane-savanna river known to receive large subsidy fluxes of terrestrial carbon and nutrients mediated by LMH, both wildlife and livestock. Using stable carbon (δ13C) and nitrogen (δ15N) isotopes, we identified spatial patterns of the relative importance of allochthonous carbon from C3 and C4 plants (woody vegetation and grasses, respectively) and autochthonous carbon from periphyton for macroinvertebrates at various sites of the Mara River and its tributaries. Potential organic carbon sources and invertebrates were sampled at 80 sites spanning stream orders 1 to 7, various catchment land uses (forest, agriculture and grasslands) and different loading rates of organic matter and nutrients by LMH (livestock and wildlife, i.e., hippopotamus). The importance of different sources of carbon along the river did not follow predictions of RCC and RPM. First, the importance of C3 and C4 carbon was not related to river order or location along the fluvial continuum but to the loading of organic matter (dung) by both wildlife and livestock. Notably, C4 carbon was important for macroinvertebrates even in large river sections inhabited by hippos. Second, even in small 1st -3rd order forested streams, autochthonous carbon was a major source of energy for macroinvertebrates, and this was fostered by livestock inputs fuelling aquatic primary production throughout the river network. Importantly, our results show that replacing wildlife (hippos) with livestock shifts river systems towards greater reliance on autochthonous carbon through an algae-grazer pathway as opposed to reliance on allochthonous inputs of C4 carbon through a detrital pathway.

scholarly journals Enrichment of Members of the Family Geobacteraceae Associated with Stimulation of Dissimilatory Metal Reduction in Uranium-Contaminated Aquifer Sediments

2002 ◽  
Vol 68 (5) ◽  
pp. 2300-2306 ◽  
Author(s):  
Dawn E. Holmes ◽  
Kevin T. Finneran ◽  
Regina A. O'Neil ◽  
Derek R. Lovley
Keyword(s):  
Microbial Community ◽  
Pcr Primers ◽  
Microbial Reduction ◽  
Most Probable Number ◽  
Probable Number ◽  
Contaminated Aquifer ◽  
Rdna Sequences ◽  
Subsurface Environments ◽  
The Family ◽  
San Juan River

ABSTRACT Stimulating microbial reduction of soluble U(VI) to insoluble U(IV) shows promise as a strategy for immobilizing uranium in uranium-contaminated subsurface environments. In order to learn more about which microorganisms might be involved in U(VI) reduction in situ, the changes in the microbial community when U(VI) reduction was stimulated with the addition of acetate were monitored in sediments from three different uranium-contaminated sites in the floodplain of the San Juan River in Shiprock, N.Mex. In all three sediments U(VI) reduction was accompanied by concurrent Fe(III) reduction and a dramatic enrichment of microorganisms in the family Geobacteraceae, which are known U(VI)- and Fe(III)-reducing microorganisms. At the point when U(VI) reduction and Fe(III) reduction were nearing completion, Geobacteraceae accounted for ca. 40% of the 16S ribosomal DNA (rDNA) sequences recovered from the sediments with bacterial PCR primers, whereas Geobacteraceae accounted for fewer than 5% of the 16S rDNA sequences in control sediments that were not amended with acetate and in which U(VI) and Fe(III) reduction were not stimulated. Between 55 and 65% of these Geobacteraceae sequences were most similar to sequences from Desulfuromonas species, with the remainder being most closely related to Geobacter species. Quantitative analysis of Geobacteraceae sequences with most-probable-number PCR and TaqMan analyses indicated that the number of Geobacteraceae sequences increased from 2 to 4 orders of magnitude over the course of U(VI) and Fe(III) reduction in the acetate-amended sediments from the three sites. No increase in Geobacteraceae sequences was observed in control sediments. In contrast to the predominance of Geobacteraceae sequences, no sequences related to other known Fe(III)-reducing microorganisms were detected in sediments. These results compare favorably with an increasing number of studies which have demonstrated that Geobacteraceae are important components of the microbial community in a diversity of subsurface environments in which Fe(III) reduction is an important process. The combination of these results with the finding that U(VI) reduction takes place during Fe(III) reduction and prior to sulfate reduction suggests that Geobacteraceae will be responsible for much of the Fe(III) and U(VI) reduction during uranium bioremediation in these sediments.

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