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A concise reference on the structural composition and function of microbial communities in coastal environments, especially in relation to natural and anthropogenic impacts. Microbial Communities in Coastal Sediments presents twenty years of coastal microbiology research, grounding it as a vital development in the field of microbial ecology. It is the first book to focus exclusively on the complex microbial ecology and its function in rest of the marine environment. The book outlines the structure, function, and assessment of microbial communities in marine sediments while exploring practical methods of assessment. It is an invaluable resource to aquatic microbiologists, marine ecologists, marine microbiologists, aquatic researchers, and graduate students in this field. Microbial Communities in Coastal Sediments begins with an examination of nutrient sources in the coastal context with a focus on organic matter inputs. The quantity and quality of organic matter in coastal sediments and their impacts on the composition and formation of microbial communities is discussed. The book explores the consequences of anthropogenic changes and human activity on microbial ecology and nutrient cycling. Sections on nutrient availability, green house gas production and biodegradation of persistent organic pollutants provide essential details. Molecular research techniques and methods for assessing microbial community structure and function in coastal sediments are also covered. Explores the interplay of physicochemical and biological features of coastal ecosystems on microbial community composition to provide a template of comparison for field research Includes unique figures, schematic diagrams and photographs related to microbial processes of coastal ecosystem to clearly represent different aspects of microbial structure and functions Provides analytical methods and detailed molecular techniques for qualitative and quantitative analyses of microbial community structure

The overall objective of the research presented here was to combine multiple geochemical parameters and molecular characterizations to provide a novel view of active microbial community ecology of sediments in a large-river deltaic estuary. In coastal and estuarine environments, a large portion of benthic respiration has been attributed to sulfate reduction and implicated as an important mechanism in hypoxia formation. The use of high-resolution sampling of individual sediment cores and high throughput nucleic acid extraction techniques combined with 454 FLX sequencing provided a robust understanding of the metabolically active benthic microbial community within coastal sediments. This was used to provide further understanding and show the importance of simultaneously analyzing the connectivity of sulfur and iron cycling to the structure and function of the microbial population. Although aqueous sulfide did not accumulate in the sediments of the northern Gulf of Mexico, active sulfate reduction was observed in all locations sampled. Microbial recycling and sequestration as iron sulfides prevented the release of sulfide from the sediment. Prominent differences were observed between the sample locations and with depth into the sediment column. This study emphasized the importance of combining novel molecular techniques with simultaneous traditional geochemical measurements to show the interdependence of microbiology and geochemistry. In addition, this study highlights the need to consider microbial community biogeography along with small-scale variations in geochemistry and biology that impact the overall cycling of redox elements when constructing biogeochemical models in marine sediments.

Anaerobic oxidation of methane (AOM) coupled to sulfate reduction (AOM-SR) is a biological process mediated by anaerobic methanotrophs (ANME) and sulfate reducing bacteria. It has scientifi c and societal relevance in regulating the global carbon cycle and biotechnological application for treating sulfate-rich wastewater. This research aimed to enhance the recent knowledge on ANME distribution and its enrichment in different bioreactor confi gurations, i.e. membrane bioreactor (MBR), biotrickling fi lter (BTF) and high pressure bioreactor (HPB). Marine sediment from Ginsburg mud volcano, Gulf of Cadiz was used as inoculum in the BTF and MBR. The BTF operation showed the enrichment of ANME in the biofi lm, especially ANME-1 (40%) and ANME-2 (10%). Whereas, the dominancy of ANME-2 and Desulfosarcina aggregates was observed in the MBR. Moreover, HPB study was performed by using highly enriched ANME-2 community from Captain Arutyunov mud volcano. During the study of HPB at different temperature and pressure conditions, the incubation at 10 MPa pressure and 15 ̊C was observed to be the most suitable condition for the studied AOM-SR community. Furthermore, AOM-SR activity in the coastal sediments from marine Lake Grevelingen (the Netherlands) was explored and the microbial community was characterised which was dominated by ANME-3 among known ANME types.

Marine sediments support complex interactions between macro-and microorganisms that have global implications for carbon and nutrient cycles. What is the state of the science on such interactions from coastal and estuarine environments to the deep sea? How does such knowledge effect environmental management? And what does future research hold in store for scientists, engineers, resource managers, and educators?Interactions between Macro- and Microorganisms in Marine Sediments responds to these questions, and more, by focusing on:? Interactions between plants, microorganisms, and marine sediment? Interactions between animals, microorganisms, and marine sediment? Interactions between macro- and microorganisms and the structuring of benthic communities? Impact of macrobenthic activity on microbially-mediated geochemical cycles in sediments? Conceptual and numeric models of diagenesis that incorporate interactions between macro- and microorganismsHere is an authoritative overview of the research, experimentation and modeling approaches now in use in our rapidly evolving understanding of life in marine sediments.

This dissertation, "Extracellular Enzymes, Microbes and Decomposition of Organic Matter in Coastal Mangrove Sediments" by Ling, Luo, 罗玲, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. Abstract: Extracellular enzymes, primarily produced by microorganisms, affect ecosystem processes because of their essential role in degradation, transformation and mineralization of organic matter. However, such data on sediments in mangrove ecosystems are especially scanty. Therefore, there is a need to investigate extracellular enzymes in mangrove ecosystems in order to estimate the C cycling dynamics on a global scale. The objectives of this research were to investigate the activities of enzymes involved in C and nutrient cycling, to assess microbial nutrient acquisition by applying enzymatic stoichiometry, to delineate the relationships among enzyme activities, microbial parameters as well as decomposition of sediment organic matter (SOM) in a coastal mangrove of Hong Kong. Strong variations in activities of hydrolases (β-glucosidase (GLU), β-N-acetyl-glucosaminidase (NAG), and acid phosphatase (ACP) involved in C, N and P cycling, respectively), but not activity of phenol oxidase (PHO, degrading recalcitrant organic matter) have been observed. However, evident variations of PHO activity were found in rhizosphere and crab-affected sediments. Hydrolase activities are positively correlated to sediment C, N and P as well as bacterial abundance, suggesting a feedback and succession of microorganisms to limitation of natural resources. On the other hand, a significant correlation between ACP and PHO activity indicates SOM degradation is controlled by P availability. Coincidentally, the enzymatic stoichiometry also suggests that this ecosystem is extremely microbial P-limited. Moreover, at molecular level, the remarkable correlations between bacterial laccase-like communities (relating to SOM degradation) and sediment C: P as well as N: P have repeatedly suggested a P-limited condition for SOM-degrading microbial communities. Therefore, it can be known that the increase of P limitation will slow down SOM decomposition and thus protect C storage in this coastal mangrove ecosystem. Furthermore, the effects of N and biochar additions on SOM decomposition have been investigated. Relative to the controls, N addition has dual role in C storage since both loss and accumulation of organic C was observed in mangrove forest and intertidal zone sediments, respectively. Sediment organic C was slightly increased after biochar addition, although the increase of PHO and GLU activity indicates a trend of C loss. This contradictory phenomenon is probably due to the entrapped or adsorbed enzymes catalyzing the oxidation or hydrolysis of SOM. Although the information is still limited on this subject, the results of this study may help to better understand the potential strategies on preventing C loss in mangrove ecosystems. Overall, the thesis indicates that SOM in this coastal mangrove is microbial P-limitation, and SOM decomposition may be slowed down so as to sequester C into sediments if microbial P limitation is exacerbated. Therefore, in further study, the importance of P in SOM degradation and microbial communities should be considered for C cycling and climate change mitigation. DOI: 10.5353/th_b5610935 Subjects: Mangrove ecology

ABSTRACT: A large fraction of the continental shelf is covered by permeable sediments that are flushed by wave, wind, and tide generated bottom currents. Elevated dissolved organic carbon (DOC) concentrations in coastal zones, a diverse and abundant sediment microbial community, and advective filtration of seawater through the surface layers of permeable sediments, make these environments important zones for the cycling of organic matter. This research investigates the role of permeable sediments in the dynamics of two central components of the carbon cycle: DOC and oxygen. In Chapter 2, published in Limnology & Oceanography, I investigate decomposition rates and compositional changes of DOC when filtered through permeable sediments contained in laboratory column reactors. Substantial amounts of DOC were mineralized in the sediments and could be linked to incorporation by aerobic and anaerobic microbes. In DOC pore-water profiles measured at two study sites with permeable sediment, we observed a concave shape of the profiles in the upper 10 cm of permeable sediment resulting from transport of DOC with advective pore water flows into the sand, and DOC decomposition in the subsurface layers. We found that the flushed sand layer between the water column and deeper anoxic sediment layers acts as an effective DOC filter, with subsurface horizontal pore-water flows promoting decomposition of DOC, suggesting that permeable sediments play a key role in the cycling of organic matter. In Chapter 3, submitted to Continental Shelf Research, I use the findings of Chapter 2 for the interpretation of field time series data of DOC, DIC, and TN concentrations in the water column and coastal sediment pore waters. We use these time series to investigate the spatial and temporal dynamics of dissolved organic matter and how benthic pelagic coupling influences DOC concentrations in the permeable sediments. Our results reveal that DOC in the upper layer (0-12 cm) of the shallow sands is controlled by benthic-pelagic coupling facilitated by advective pore water filtration modulated by the regional wave climate. For the quantification of oxygen fluxes in the permeable coastal sands resulting from the benthic organic matter production and consumption and the current-induced sediment flushing, I deployed the eddy correlation technique. In order to make this technique more suitable for our shallow coastal zone with relatively rough hydrodynamic conditions (as compared to deeper marine environments), we adapted existing eddy correlation instruments for use with more durable and repairable oxygen optodes. This development is described in detail in Chapter 4 that has been submitted for publication in Limnology and Oceanography Methods. Our results show that optodes have a comparable response time to electrodes, produce similar fluxes in field deployments, and are a viable alternative for use with the eddy correlation measurement in coastal environments with strong currents and wave action. These hydrodynamic conditions are an important factor controlling production and decomposition processes at the sediment-water interface and within the sediment because they can largely control the availability of DOC and oxygen to microbial communities in the sediments. In Chapter 5, which is presently is being prepared for submission to Marine Ecology - Progress Series, we investigate the relationship between flow, wave height, DOC concentration, temperature, light, and the benthic oxygen fluxes. The results reveal a large range of production and consumption rates in the permeable coastal sediments with distinct seasonal changes. The latter are caused by the availability of degradable organic matter and the magnitude of the pore water flushing process that carries these organic substrates and oxygen into the permeable coastal sands. We conclude that the highly degradable DOC produced by pelagic and benthic primary producers enhances water column - sediment biogeochemical coupling in the coastal zone thereby increasing the contribution of the sediment surface layer in the cycling of carbon and nutrients.

Abstract: The Red Sea is one of the most unique environments worldwide. It possesses a unique geography, physical, chemical and biological characteristics. It encounters several ecosystems articulating with each other, these include, corals, mangroves, algae, fisheries, invertebrates and microbiota of each one of these along with microbiota of the Red Sea waters and sediments. Studying the collective microbial communities of the Egyptian Red Sea coastal sediments have not been reported before. In regards to the severe pollution impacting the different Red Sea ecosystems, sediments samples have been collected from different impacted sites. The selected sites included 1- four ports for shipping aluminum, ilmenite and phosphate, 2-a site previously reported to have suffered extensive oil spills, 3-a reported tourism impacted site 4- two mangrove sites and 5-two lakes. Bacterial communities for each site have been studied through two different approaches, Culture-Dependent and Culture-Independent approaches. Pyrosequencing of V6-V4 hypervariable regions of 16S rDNA, isolated through the two approaches, has been used to assess the microbial community of each site. Physical parameters, Chemical analysis for 29 elements, selected semi-volatile oil contents, along with Carbon, Hydrogen, Nitrogen and Sulfur (CHNS) contents have been measured for each site. 131,402 and 136,314 significant reads have been generated through the Culture-Dependent and Independent approaches, respectively. Generally, Proteobacteria, Firmicutes, Actinobateria, Fusobacteria, Gemmatimonadetes and Bacteriodetes are the major bacterial groups detected through the two approaches. The Culture-Dependent datasets distinctive analysis revealed three main patterns (1) marine Vibrio spp.-suggesting a "marine Vibrio phenomenon"; (2) potential human pathogens; and (3) oil-degrading bacteria. While the Culture-Independent datasets analysis reported (1) an Egyptian Red Sea Coastal Microbiome, taxa detected in all the sites and (2) Hydrocarbon biodegrading bacteria predominance to the majority of the sites; particularly in two ports. On the other hand, the two lakes, through the two approaches, showed unique bacterial patterns, which generally grouped into anaerobic, halophilic and sulfur metabolizing bacteria. Individually, sites showed unique evolution of their microbial communities based on minor intrinsic and imposed variation per sites. Our results draw attention to the effects of different sources of pollution on the Red Sea and suggest the need for further analysis to overcome the hazardous effects observed at the impacted sites.

This project was begun in July 1988 as part of Phase I of the Deep Microbiology Subprogram. At this time, the Subprogram was preparing for sampling near the Savannah River Site (SRS) from what was being termed the ''Investigator's Hole.'' This was the fourth hole drilled for sampling in the coastal plain sediments at a site near the SRS. Since there was a possibility of sampling from the saline Triassic basin in the deeper regions in this fourth hole, there was particular interest in quantifying halotolerant microorganisms from these samples and in determining the responses of subsurface microbes to a range of soft concentrations. Further interest in the soft tolerances of microbes from these coastal sediments arose from the fact that all of these sediments were deposited under marine conditions. It was also anticipated that samples would be available from the shallow unsaturated (vadose) zone at this site, so there was interest in quantifying microbial responses to matric water potential as well as solute water potential. The initial objectives of this research project were to: characterize microbial communities in a saline aquifer; determine the potential for microbial metabolism of selected organic compounds in a saline aquifers; characterize microbial communities in unsaturated subsurface materials (vadose zones); and determine the potential for microbial metabolism of selected organic compounds in unsaturated subsurface materials (vadose zones). Samples were collected from the borehole during a period extending from August to October 1988. A total of nine samples were express shipped to New Mexico Tech for analyses. These were all saturated zone samples from six different geological formations. Water contents and water potentials were measured at the time of sample arrival.

This project was begun in July 1988 as part of Phase I of the Deep Microbiology Subprogram. At this time, the Subprogram was preparing for sampling near the Savannah River Site (SRS) from what was being termed the Investigator's Hole.'' This was the fourth hole drilled for sampling in the coastal plain sediments at a site near the SRS. Since there was a possibility of sampling from the saline Triassic basin in the deeper regions in this fourth hole, there was particular interest in quantifying halotolerant microorganisms from these samples and in determining the responses of subsurface microbes to a range of soft concentrations. Further interest in the soft tolerances of microbes from these coastal sediments arose from the fact that all of these sediments were deposited under marine conditions. It was also anticipated that samples would be available from the shallow unsaturated (vadose) zone at this site, so there was interest in quantifying microbial responses to matric water potential as well as solute water potential. The initial objectives of this research project were to: characterize microbial communities in a saline aquifer; determine the potential for microbial metabolism of selected organic compounds in a saline aquifers; characterize microbial communities in unsaturated subsurface materials (vadose zones); and determine the potential for microbial metabolism of selected organic compounds in unsaturated subsurface materials (vadose zones). Samples were collected from the borehole during a period extending from August to October 1988. A total of nine samples were express shipped to New Mexico Tech for analyses. These were all saturated zone samples from six different geological formations. Water contents and water potentials were measured at the time of sample arrival.

Anaerobic oxidation of methane (AOM) coupled to sulfate reduction (AOM-SR) is a biological process mediated by anaerobic methanotrophs (ANME) and sulfate reducing bacteria. It has scientifi c and societal relevance in regulating the global carbon cycle and biotechnological application for treating sulfate-rich wastewater. This research aimed to enhance the recent knowledge on ANME distribution and its enrichment in different bioreactor confi gurations, i.e. membrane bioreactor (MBR), biotrickling fi lter (BTF) and high pressure bioreactor (HPB). Marine sediment from Ginsburg mud volcano, Gulf of Cadiz was used as inoculum in the BTF and MBR. The BTF operation showed the enrichment of ANME in the biofi lm, especially ANME-1 (40%) and ANME-2 (10%). Whereas, the dominancy of ANME-2 and Desulfosarcina aggregates was observed in the MBR. Moreover, HPB study was performed by using highly enriched ANME-2 community from Captain Arutyunov mud volcano. During the study of HPB at different temperature and pressure conditions, the incubation at 10 MPa pressure and 15 ̊C was observed to be the most suitable condition for the studied AOM-SR community. Furthermore, AOM-SR activity in the coastal sediments from marine Lake Grevelingen (the Netherlands) was explored and the microbial community was characterised which was dominated by ANME-3 among known ANME types.

We investigated the changes of the bacterial community to treatment of Mississippi Canyon Macondo oil (MC252) in Gulf of Mexico (GoM) coastal sediment microcosms collected from Bayou La Batre, Dauphin Island, Petit Bois Island, and Perdido Pass. We utilized molecular methods by targeting the V3 - V5 region of the 16S rRNA gene from metacommunity DNA through culture-dependent and culture-independent (Bacterial Tag -encoded FLX Amplified Pyrosequencing ; bTEFAP) methodologies and downstream bioinformatics tools. Through bTEFAP, we generated a total of 11,338 (Bayou La Batre) and 38,104 (Dauphin Island, Petit Bois Island, and Perdido Pass) reads. After quality-based trimming, a total of 8,430 (Bayou La Batre) and 36,520 (Dauphin Island, Petit Bois Island, and Perdido Pass) quality reads remained. Following quality checking, analyses of the bTEFAP data determined that the microbial assemblages of all 4 locations showed changes to the oil treatment. The phyla Proteobacteria, Bacteroidetes, and Firmicutes all increased with treatment of oil and thus may play an important role in biodegradation and bioremediation of oil. In particular, within the phylum Proteobacteria, the class Gammaproteobacteria appeared to be the dominant bacterial taxon in the oil treated samples. Moreover, we were able to identify microbial taxa that associated with early response, early transient response , and late response in relation to oil treatment. In order to investigate the presence of biodegradative genes, we conducted PCR to detect the presence of biodegradative genes in all 4 sample sites. Our results showed the amplification of biodegradative genes such as alkane hydroxylase (alkB870G), catechol 2,3 dioxygenase (C23DO, and Cat2,3 1a) and biphenyl dioxygenase (bphA1) in oil treated sediments. Furthermore, we isolated a consortium of bacterial isolates: Exiguobacterium, Pseudoalteromonas, Halomonas and Dyadobacter that carried hydrocarbon-degrading genes such as alkane hydroxylase (Rh - alkB1, Rh - alkB2, and alkB870G) , the ISP [alpha] subunit of naphthalene dioxygenase (doB ), C23DO, Cat2,3 1a, and bphA1. Collectively, our results indicated that the indigenous bacterial communities in all 4 different sampling locations responded quickly to the addition of MC252 oil and as a result, the bacterial community structure altered selectively for hydrocarbonocalstic taxa that possess biodegradation activity of oil in the GoM ecosystem.

Biodegradation mediated by indigenous microbial communities is the ultimate fate of the majority of oil hydrocarbon that enters the marine environment. The aim of this Research Topic is to highlight recent advances in our knowledge of the pathways and controls of microbially-catalyzed hydrocarbon degradation in marine ecosystems, with emphasis on the response of microbial communities to the Deepwater Horizon oil spill in the Gulf of Mexico. In this Research Topic, we encouraged original research and reviews on the ecology of hydrocarbon-degrading bacteria, the rates and mechanisms of biodegradation, and the bioremediation of discharged oil under situ as well as near in situ conditions.

This book presents a summary of terrestrial microbial processes, which are a key factor in supporting healthy life on our planet. The authors explain how microorganisms maintain the soil ecosystem through recycling carbon and nitrogen and then provide insights into how soil microbiology processes integrate into ecosystem science, helping to achieve successful bioremediation as well as safe and effective operation of landfills, and enabling the design of composting processes that reduce the amount of waste that is placed in landfills. The book also explores the effect of human land use, including restoration on soil microbial communities and the response of wetland microbial communities to anthropogenic pollutants. Lastly it discusses the role of fungi in causing damaging, and often lethal, infectious diseases in plants and animals.

A survey of marine sediment microbial populations to determine what microorganisms are present and what their metabolic capability is for degradation of model petroleum hydrocarbons. The effect of sediment on bioavailability of a polycyclic aromatic hydrocarbon (phenanthrene) to hydrocarbon-degrading bacteria was also examined. Sampling locations included areas offshore Barrow and Prudhoe Bay, Elson Lagoon, and three rivers.