Nitrifier and denitrifier molecular operational taxonomic unit compositions from sites of a freshwater estuary of Chesapeake Bay

Temporal and spatial changes in the molecular operational taxonomic unit (OTU) compositions of bacteria harboring genes for nitrification and denitrification were assessed using denaturing gradient gel electrophoresis (DGGE), clone-based DNA sequencing of selected PCR products, and analyses of ammonium and organic matter concentrations. Sediment, overlying water, and pore-water samples were taken from different vegetated sites of Jug Bay National Estuarine Research Reserve, Maryland, during spring, summer, and fall 2006. OTU richness and the diversities of nitrifiers and denitrifiers were assessed by the presence of bands on DGGE gels, both ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) were seasonally dependent. AOB OTU richness was highest in the summer when NOB richness was decreased, whereas NOB richness was highest in the spring when AOB richness was decreased. The OTU diversities of nitrifiers did not correlate with ammonium concentrations, organic matter concentrations, or the presence of vegetation. The OTU diversities of denitrifiers possessing either the nirK or nosZ genes were not seasonally dependent but were positively correlated with organic matter content (p = 0.0015, r2 = 0.27; p < 0.0001, r2 = 0.39, respectively). Additionally, the presence of vegetation significantly enhanced nosZ species richness (Wilcoxon/Kruskal–Wallis test, p < 0.008), but this trend was not seen for nirK OTU richness. Banding patterns for nirK OTUs were more similar within sites for each season compared with any of the other genes. Over all seasons, nirK OTU richness was highest and AOB and nosZ OTU richness were lowest (Wilcoxon/Kruskal–Wallis test, p < 0.0001). High levels of sequence divergence among cloned nirK PCR products indicate a broad diversity of nirK homologs in this freshwater estuary.

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Molecular Analysis of Ammonia-Oxidizing Bacteria of the β Subdivision of the Class Proteobacteria in Compost and Composted Materials

Applied and Environmental Microbiology ◽

10.1128/aem.65.2.396-403.1999 ◽

1999 ◽

Vol 65 (2) ◽

pp. 396-403 ◽

Cited By ~ 159

Author(s):

George A. Kowalchuk ◽

Zinaida S. Naoumenko ◽

Piet J. L. Derikx ◽

Andreas Felske ◽

John R. Stephen ◽

...

Keyword(s):

Denaturing Gradient Gel Electrophoresis ◽

Ammonia Oxidizer ◽

Ammonia Oxidizing Bacteria ◽

Nitrogen Transformations ◽

Rt Pcr ◽

Gene Encoding ◽

Specific Pcr ◽

Pcr Products ◽

Gradient Gel Electrophoresis ◽

Almost All

ABSTRACT Although the practice of composting animal wastes for use as biofertilizers has increased in recent years, little is known about the microorganisms responsible for the nitrogen transformations which occur in compost and during the composting process. Ammonia is the principle available nitrogenous compound in composting material, and the conversion of this compound to nitrite in the environment by chemolithotrophic ammonia-oxidizing bacteria is an essential step in nitrogen cycling. Therefore, the distribution of ammonia-oxidizing members of the β subdivision of the class Proteobacteriain a variety of composting materials was assessed by amplifying 16S ribosomal DNA (rDNA) and 16S rRNA by PCR and reverse transcriptase PCR (RT-PCR), respectively. The PCR and RT-PCR products were separated by denaturing gradient gel electrophoresis (DGGE) and were identified by hybridization with a hierarchical set of oligonucleotide probes designed to detect ammonia oxidizer-like sequence clusters in the genera Nitrosospira and Nitrosomonas. Ammonia oxidizer-like 16S rDNA was detected in almost all of the materials tested, including industrial and experimental composts, manure, and commercial biofertilizers. A comparison of the DGGE and hybridization results after specific PCR and RT-PCR suggested that not all of the different ammonia oxidizer groups detected in compost are equally active. amoA, the gene encoding the active-site-containing subunit of ammonia monooxygenase, was also targeted by PCR, and template concentrations were estimated by competitive PCR. Detection of ammonia-oxidizing bacteria in the composts tested suggested that such materials may not be biologically inert with respect to nitrification and that the fate of nitrogen during composting and compost storage may be affected by the presence of these organisms.

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Warming increases carbon-nutrient fluxes from sediments in streams across land use

Biogeosciences Discussions ◽

10.5194/bgd-9-11293-2012 ◽

2012 ◽

Vol 9 (8) ◽

pp. 11293-11330

Author(s):

S.-W. Duan ◽

S. S. Kaushal

Keyword(s):

Land Use ◽

Organic Matter ◽

Sulfate Reduction ◽

Organic Matter Content ◽

Soluble Reactive Phosphorus ◽

Matter Content ◽

Overlying Water ◽

Watershed Land Use ◽

Sediment Fluxes

Abstract. Rising water temperatures due to climate and land-use change can accelerate biogeochemical fluxes from sediments to streams. We investigated impacts of increased streamwater temperatures on sediment fluxes of dissolved organic carbon (DOC), nitrate, soluble reactive phosphorus (SRP) and sulfate. Experiments were conducted at 8 long-term monitoring sites across land use (forest, agricultural, suburban, and urban) at the Baltimore Ecosystem Study Long-Term Ecological Research (LTER) site in the Chesapeake Bay watershed. Over 20 yr of routine water temperature data showed substantial variation across seasons and years, and lab incubations were conducted at 4 temperatures (4 °C, 15 °C, 25 °C and 35 °C) for 48 h. Results indicated: (1) warming consistently increased sediment DOC fluxes to overlying water across land use but decreased DOC quality via increases in the humic-like to protein-like fractions (2) warming consistently increased SRP fluxes from sediments to overlying water across land use (3) warming increased sulfate fluxes from sediments to overlying water at rural/suburban sites but decreased sulfate fluxes at urban sites likely due to sulfate reduction (4) nitrate fluxes showed an increasing trend with temperature but with larger variability than SRP. Sediment fluxes of nitrate, SRP and sulfate were strongly related to watershed urbanization and organic matter content. Using relationships of sediment fluxes with temperature, we estimate a 5 °C warming would increase the annual sediment release by 1.0–3.9 times. In addition to hydrologic variability, understanding warming impacts on coupled biogeochemical cycles in streams (e.g., organic matter mineralization, P sorption, nitrification, denitrification, and sulfate reduction) is critical for forecasting changes in carbon and nutrient exports across watershed land use.

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Organic matter increases jarosite dissolution in acid sulfate soils under inundation conditions

Soil Research ◽

10.1071/sr05096 ◽

2006 ◽

Vol 44 (1) ◽

pp. 11 ◽

Cited By ~ 12

Author(s):

Chengxing Chu ◽

Chuxia Lin ◽

Yonggui Wu ◽

Wenzhou Lu ◽

Jie Long

Keyword(s):

Organic Matter ◽

Organic Matter Content ◽

Column Experiment ◽

Matter Content ◽

Overlying Water ◽

Experimental Conditions ◽

Acid Sulfate ◽

Reducing Conditions ◽

The Stability ◽

Sulfate Soils

A column experiment was conducted to examine the effects of added organic matter and thickness of surface water on the stability of jarosite in a coastal acid sulfate soil. The results show that dissolution of jarosite was negligible if no organic matter was added onto the soil. However, where organic matter was added onto the soils, the acidity and the concentrations of iron and sulfate in the leachate of the soil increased following water inundation, indicating the decomposition of jarosite in such conditions. Probably, the organic matter content of the soil was originally too low to enable the creation of reducing conditions that could sufficiently cause the breakdown of jarosite contained in the soil. Under the experimental conditions, the amount of added organic matter played a more important role than the thickness of the overlying water in the dissolution of jarosite.

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Cold Adapted Nitrosospira sp.: A Potential Crucial Contributor of Ammonia Oxidation in Cryosols of Permafrost-Affected Landscapes in Northeast Siberia

Microorganisms ◽

10.3390/microorganisms7120699 ◽

2019 ◽

Vol 7 (12) ◽

pp. 699 ◽

Cited By ~ 1

Author(s):

Tina Sanders ◽

Claudia Fiencke ◽

Jennifer Hüpeden ◽

Eva Maria Pfeiffer ◽

Eva Spieck

Keyword(s):

Organic Matter ◽

Ammonia Oxidation ◽

Inorganic Nitrogen ◽

Organic Matter Content ◽

Matter Content ◽

Organic Soils ◽

Ammonia Oxidizing Bacteria ◽

Cold Adapted ◽

Oxidation Rates ◽

North East

Permafrost-affected landscape soils are rich in organic matter and contain a high fraction of organic nitrogen, but much of this organic matter remains inaccessible due to nitrogen limitation. Microbial nitrification is a key process in the nitrogen cycle, controlling the availability of dissolved inorganic nitrogen (DIN) such as ammonium and nitrate. In this study, we investigate the microbial diversity of canonical nitrifiers and their potential nitrifying activity in the active layer of different Arctic cryosols in the Lena River Delta in North-East Siberia. These cryosols are located on Samoylov Island, which has two geomorphological landscapes with mineral soils in the modern floodplain and organic-rich soils in the low-centered polygonal tundra of the Holocene river terrace. Microcosm incubations show that the highest potential ammonia oxidation rates are found in low organic soils, and the rates depend on organic matter content and quality, vegetation cover, and water content. As shown by 16S rRNA amplicon sequencing, nitrifiers represented 0.6% to 6.2% of the total microbial community. More than 50% of the nitrifiers belonged to the genus Nitrosospira. Based on PCR amoA analysis, ammonia-oxidizing bacteria (AOB) were found in nearly all soil types, whereas ammonia-oxidizing archaea (AOA) were only detected in low-organic soils. In cultivation-based approaches, mainly Nitrosospira-like AOB were enriched and characterized as psychrotolerant, with temperature optima slightly above 20 °C. This study suggests a ubiquitous distribution of ammonia-oxidizing microorganisms (bacteria and archaea) in permafrost-affected landscapes of Siberia with cold-adapted AOB, especially of the genus Nitrosospira, as potentially crucial ammonia oxidizers in the cryosols.

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Biological Reduction of Organic Matter in Buji River Sediment (Shenzhen, China) with Artificial Oxygenation

Water ◽

10.3390/w12123592 ◽

2020 ◽

Vol 12 (12) ◽

pp. 3592

Author(s):

Lin Che ◽

Wenbiao Jin ◽

Xu Zhou ◽

Chenbo Cao ◽

Wei Han ◽

...

Keyword(s):

Organic Matter ◽

River Sediment ◽

Water Injection ◽

Organic Matter Content ◽

Matter Content ◽

Urban River ◽

Pure Oxygen ◽

Overlying Water ◽

Biological Reduction ◽

Do Concentration

In this work, artificial oxygenation treatment (pure oxygen aeration or oxygen enriched water injection) combined with the introduction of exogenous microorganisms was employed to purify urban river sediment for the first time. Results showed that the developed in situ remediation strategy could increase the dissolved oxygen (DO) concentration and oxidation-reduction potential (ORP) value of the sediments. Benefiting from the increase of DO concentration, the bacterial diversity was enhanced. The highest removal efficiencies of organic matter were 18.4% and 22.3% through pure oxygen aeration and oxygen enriched water injection, respectively. More importantly, overlying water quality was not affected. By comparison, oxygen enriched water injection treatment could achieve better performance on sediment purification. Introducing exogenous microorganisms further reduced the organic matter content of the sediment. In short, the current work not only proposed a promising strategy for controlling urban river sediment pollution, but also provided novel insight for the understanding of river sediment containing highly concentrated organic matter.

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HEAVY METAL SPECIATION IN BOTTOM SEDIMENTS OF THE VYSHNEVOLOTSKY RESERVOIR

Moscow University Bulletin. Series 4. Geology ◽

10.33623/0579-9406-2018-3-46-54 ◽

2018 ◽

pp. 46-54

Author(s):

O. A. Lipatnikova

Keyword(s):

Heavy Metal ◽

Organic Matter ◽

Bottom Sediments ◽

Metal Speciation ◽

Organic Matter Content ◽

Water Reservoir ◽

Matter Content ◽

Heavy Metal Speciation ◽

Mobile Forms ◽

Manganese Hydroxides

The study of heavy metal speciation in bottom sediments of the Vyshnevolotsky water reservoir is presented in this paper. Sequential selective procedure was used to determine the heavy metal speciation in bottom sediments and thermodynamic calculation — to determine ones in interstitial water. It has been shown that Mn are mainly presented in exchangeable and carbonate forms; for Fe, Zn, Pb и Co the forms are related to iron and manganese hydroxides is played an important role; and Cu and Ni are mainly associated with organic matter. In interstitial waters the main forms of heavy metal speciation are free ions for Zn, Ni, Co and Cd, carbonate complexes for Pb, fulvate complexes for Cu. Effects of particle size and organic matter content in sediments on distribution of mobile and potentially mobile forms of toxic elements have been revealed.

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Changes in organic matter content of soil as a result of long-term fertilization

Cereal Research Communications ◽

10.1556/crc.33.2005.1.12 ◽

2005 ◽

Vol 33 (1) ◽

pp. 53-55

Author(s):

Katalin Berecz ◽

Katalin Debreczeni

Keyword(s):

Organic Matter ◽

Organic Matter Content ◽

Matter Content

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Physico-Chemical Properties of Soil Collected from Chandrabhaga River in Kalmeshwar, Nagpur, Maharashtra

Journal of Advanced Research in Alternative Energy Environment and Ecology ◽

10.24321/2455.3093.202006 ◽

2020 ◽

Vol 07 (02) ◽

pp. 1-3

Author(s):

Amita M Watkar ◽

Keyword(s):

Organic Matter ◽

Soil Quality ◽

Agricultural Land ◽

Organic Matter Content ◽

Chemical Properties ◽

Matter Content ◽

Soil Attributes ◽

Essential Components ◽

Agricultural Land Management ◽

Physical And Chemical

Soil, itself means Soul of Infinite Life. Soil is the naturally occurring unconsolidated or loose covering on the earth’s surface. Physical properties depend upon the amount, size, shape, arrangement, and mineral composition of soil particles. It also depends on the organic matter content and pore spaces. Chemical properties depend on the Inorganic and organic matter present in the soil. Soils are the essential components of the environment and foundation resources for nearly all types of land use, besides being the most important component of sustainable agriculture. Therefore, assessment of soil quality and its direction of change with time is an ideal and primary indicator of sustainable agricultural land management. Soil quality indicators refer to measurable soil attributes that influence the capacity of a soil to function, within the limits imposed by the ecosystem, to preserve biological productivity and environmental quality and promote plant, animal and human health. The present study is to assess these soil attributes such as physical and chemical properties season-wise.

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