scholarly journals Oyster calcifying fluid harbors persistent and dynamic autochthonous bacterial populations that may aid in shell formation

2020 ◽  
Vol 653 ◽  
pp. 57-75
Author(s):  
EG Sakowski ◽  
KE Wommack ◽  
SW Polson
Keyword(s):  
Microbial Communities ◽  
Water Column ◽  
Nitrate Reduction ◽  
Keystone Species ◽  
Eastern Oyster ◽  
Shell Formation ◽  
Calcium Carbonate Precipitation ◽  
Bacterial Populations ◽  
The Impact

The eastern oyster Crassostrea virginica is a keystone species in estuarine environments but faces threats to shell formation associated with warming temperatures and ocean acidification. Extrapallial fluid (EF), which is responsible for shell formation, harbors diverse and abundant microbial communities. Commensal microbial communities are vital to host health and fitness, yet long-term studies investigating temporal responses of the EF microbiome and its function in oyster fitness are lacking. In this study, bacterial communities of oyster EF and the water column were characterized monthly from October 2010 to September 2011. We investigated the selection, composition, and dynamics of resident and transient community members, evaluated the impact of temperature on EF microbial communities, and examined the functional role of the EF microbiome. Oyster EF communities were significantly different from those of the water column and were enriched for several taxa, including the Deltaproteobacteria, Epsilonproteobacteria, and Gammaproteobacteria. Overall, 94 resident members were identified in oyster EF. These members were persistent and abundant, comprising on average 33% of EF communities. Resident EF communities formed high-temperature and low-temperature groups and were more abundant overall at colder temperatures. Oyster EF resident communities were predicted to be enriched for dissimilatory nitrate reduction, nitrogen fixation, nitrification, and sulfite reductase genes. Sulfate and nitrate reduction may have a synergistic effect on calcium carbonate precipitation and indirectly aid in shell formation. Therefore, the potential role of the oyster EF microbiome in shell formation warrants further investigation as oysters and other shellfish face the future impacts of ocean warming and acidification.

Protozoa abundance, growth, and bacterivory in the water column, on sedimenting particles, and in the sediment of Halifax Harbor

1990 ◽  
Vol 36 (12) ◽  
pp. 859-863 ◽  
Author(s):  
James A. Novitsky
Keyword(s):  
Bacterial Community ◽  
Water Column ◽  
Sediment Surface ◽  
Metabolic Inhibitor ◽  
Optimum Conditions ◽  
Bacterial Populations ◽  
Protozoan Grazing ◽  
Large Numbers ◽  
Doubling Times

The role of protozoan grazing in controlling bacterial populations was examined in four microbial habitats in Halifax Harbor, Canada: the water column, setting particles, the sediment–water interface, and the sediment. Large numbers of protozoans were found in all habitats although most (>56%) were small (<5 μm) flagellates. Protozoans larger than 10 μm were rarely observed; protozoans >20 μm were never observed. Protozoans were also observed to a depth of 9 cm below the sediment surface although efforts to culture viable protozoa failed except for the top 1 cm. The use of the metabolic inhibitor cycloheximide with and without colchicine to selectively inhibit eucaryotic metabolism was shown to severely affect procaryotic metabolism in sediment (and presumably particle and water) samples. Using fluorescently labelled bacteria as food, and under optimum conditions, up to 42% of the Protozoa population exhibited active grazing within 7 h. Using protozoan and bacterial community sizes and doubling times, it was calculated that each protozoan in Halifax Harbor would have to consume 13–118 bacteria per hour for the enumerated nanoplanktonic (<20 μm) Protozoa to be the sole control of the size of the bacterial community. Key words: marine, Protozoa, bacterivory, particles, bacteria.

scholarly journals Increasing sulfate levels show a differential impact on synthetic communities comprising different methanogens and a sulfate reducer

2019 ◽  
Vol 16 (154) ◽  
pp. 20190129 ◽  
Author(s):  
Jing Chen ◽  
Matthew J. Wade ◽  
Jan Dolfing ◽  
Orkun S. Soyer
Keyword(s):  
Microbial Communities ◽  
Methane Production ◽  
System Stability ◽  
Sulfate Reducer ◽  
Differential Impact ◽  
Sulfate Reducers ◽  
Hydrogenotrophic Methanogens ◽  
The Stability ◽  
The Impact

Methane-producing microbial communities are of ecological and biotechnological interest. Syntrophic interactions among sulfate reducers and aceto/hydrogenotrophic and obligate hydrogenotrophic methanogens form a key component of these communities, yet, the impact of these different syntrophic routes on methane production and their stability against sulfate availability are not well understood. Here, we construct model synthetic communities using a sulfate reducer and two types of methanogens representing different methanogenesis routes. We find that tri-cultures with both routes increase methane production by almost twofold compared to co-cultures and are stable in the absence of sulfate. With increasing sulfate, system stability and productivity decreases and does so faster in communities with aceto/hydrogenotrophic methanogens despite the continued presence of acetate. We show that this is due to a shift in the metabolism of these methanogens towards co-utilization of hydrogen with acetate. These findings indicate the important role of hydrogen dynamics in the stability and productivity of syntrophic communities.

scholarly journals Molecular Hydrogen, a Neglected Key Driver of Soil Biogeochemical Processes

2019 ◽  
Vol 85 (6) ◽  
Author(s):  
Sarah Piché-Choquette ◽  
Philippe Constant
Keyword(s):  
Energy Requirement ◽  
Keystone Species ◽  
Physiological Role ◽  
Atp Synthesis ◽  
Potential Contribution ◽  
Biogeochemical Processes ◽  
Individual Level ◽  
C Cycling ◽  
The Impact

ABSTRACTThe atmosphere of the early Earth is hypothesized to have been rich in reducing gases such as hydrogen (H2). H2has been proposed as the first electron donor leading to ATP synthesis due to its ubiquity throughout the biosphere as well as its ability to easily diffuse through microbial cells and its low activation energy requirement. Even today, hydrogenase enzymes enabling the production and oxidation of H2are found in thousands of genomes spanning the three domains of life across aquatic, terrestrial, and even host-associated ecosystems. Even though H2has already been proposed as a universal growth and maintenance energy source, its potential contribution as a driver of biogeochemical cycles has received little attention. Here, we bridge this knowledge gap by providing an overview of the classification, distribution, and physiological role of hydrogenases. Distribution of these enzymes in various microbial functional groups and recent experimental evidence are finally integrated to support the hypothesis that H2-oxidizing microbes are keystone species driving C cycling along O2concentration gradients found in H2-rich soil ecosystems. In conclusion, we suggest focusing on the metabolic flexibility of H2-oxidizing microbes by combining community-level and individual-level approaches aiming to decipher the impact of H2on C cycling and the C-cycling potential of H2-oxidizing microbes, via both culture-dependent and culture-independent methods, to give us more insight into the role of H2as a driver of biogeochemical processes.

Water management and phenology influence the root-associated rice field microbiota

2020 ◽  
Vol 96 (9) ◽  
Author(s):  
Matteo Chialva ◽  
Stefano Ghignone ◽  
Paolo Cozzi ◽  
Barbara Lazzari ◽  
Paola Bonfante ◽  
...  
Keyword(s):  
Water Management ◽  
Microbial Communities ◽  
Rice Field ◽  
Water Status ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Upland Conditions ◽  
The Impact ◽  
Comprehensive Study

ABSTRACT Microbial communities associated with plants are greatly influenced by water availability in soil. In flooded crops, such as rice, the impact of water management on microbial dynamics is not fully understood. Here, we present a comprehensive study of the rice microbiota investigated in an experimental field located in one of the most productive areas of northern Italy. The microbiota associated with paddy soil and root was investigated using 454 pyrosequencing of 16S, ITS and 18S rRNA gene amplicons under two different water managements, upland (non-flooded, aerobic) and lowland (traditional flooding, anaerobic), at three plant development stages. Results highlighted a major role of the soil water status in shaping microbial communities, while phenological stage had low impacts. Compositional shifts in prokaryotic and fungal communities upon water management consisted in significant abundance changes of Firmicutes, Methanobacteria, Chloroflexi, Sordariomycetes, Dothideomycetes and Glomeromycotina. A vicariance in plant beneficial microbes and between saprotrophs and pathotrophs was observed between lowland and upland. Moreover, through network analysis, we demonstrated different co-abundance dynamics between lowland and upland conditions with a major impact on microbial hubs (strongly interconnected microbes) that fully shifted to aerobic microbes in the absence of flooding.

scholarly journals THE ROLE OF MICROBIAL COMMUNITIES OF AIRWAYS IN PATHOGENESIS OF CHRONIC OBSTRUCTIVE PULMONARY DISEASE

2014 ◽  
Vol 13 (1) ◽  
pp. 153-160 ◽  
Author(s):  
S. V. Fedosenko ◽  
L. M. Ogorodova ◽  
M. A. Karnaushkina ◽  
Ye. S. Kulikov ◽  
I. A. Deyev ◽  
...  
Keyword(s):  
Chronic Obstructive Pulmonary Disease ◽  
Microbial Communities ◽  
Pulmonary Disease ◽  
Molecular Genetic ◽  
Genetic Identification ◽  
Current Therapy ◽  
Chronic Obstructive ◽  
Obstructive Pulmonary Disease ◽  
The Impact

This review summarizes the results of studies on the composition of microbial communities in the airways of healthy subjects and in patients with chronic obstructive pulmonary disease. Modern technologies of molecular-genetic identification methods of microorganisms allow to perform a deep analysis  of  the  respiratory  microbiom.  It  is  of  considerable  interest  to  determine  the  role  of  the microbiome in the development of human diseases of the bronchopulmonary system, and to understand the impact of the microbes communities as a course of disease and the important factor for the efficacy of current therapy.

scholarly journals The fate of fixed nitrogen in marine sediments with low organic loading: an in situ study

2017 ◽  
Vol 14 (2) ◽  
pp. 285-300 ◽  
Author(s):  
Stefano Bonaglia ◽  
Astrid Hylén ◽  
Jayne E. Rattray ◽  
Mikhail Y. Kononets ◽  
Nils Ekeroth ◽  
...  
Keyword(s):  
Baltic Sea ◽  
Water Column ◽  
Nitrate Reduction ◽  
Organic N ◽  
Fixed Nitrogen ◽  
Coastal Station ◽  
Solute Fluxes ◽  
The Baltic ◽  
The Impact

Abstract. Over the last decades, the impact of human activities on the global nitrogen (N) cycle has drastically increased. Consequently, benthic N cycling has mainly been studied in anthropogenically impacted estuaries and coasts, while in oligotrophic systems its understanding is still scarce. Here we report on benthic solute fluxes and on rates of denitrification, anammox, and dissimilatory nitrate reduction to ammonium (DNRA) studied by in situ incubations with benthic chamber landers during two cruises to the Gulf of Bothnia (GOB), a cold, oligotrophic basin located in the northern part of the Baltic Sea. Rates of N burial were also inferred to investigate the fate of fixed N in these sediments. Most of the total dissolved fixed nitrogen (TDN) diffusing to the water column was composed of organic N. Average rates of dinitrogen (N2) production by denitrification and anammox (range: 53–360 µmol N m−2 day−1) were comparable to those from Arctic and subarctic sediments worldwide (range: 34–344 µmol N m−2 day−1). Anammox accounted for 18–26 % of the total N2 production. Absence of free hydrogen sulfide and low concentrations of dissolved iron in sediment pore water suggested that denitrification and DNRA were driven by organic matter oxidation rather than chemolithotrophy. DNRA was as important as denitrification at a shallow, coastal station situated in the northern Bothnian Bay. At this pristine and fully oxygenated site, ammonium regeneration through DNRA contributed more than one-third to the TDN efflux and accounted, on average, for 45 % of total nitrate reduction. At the offshore stations, the proportion of DNRA in relation to denitrification was lower (0–16 % of total nitrate reduction). Median value and range of benthic DNRA rates from the GOB were comparable to those from the southern and central eutrophic Baltic Sea and other temperate estuaries and coasts in Europe. Therefore, our results contrast with the view that DNRA is negligible in cold and well-oxygenated sediments with low organic carbon loading. However, the mechanisms behind the variability in DNRA rates between our sites were not resolved. The GOB sediments were a major source (237 kt yr−1, which corresponds to 184 % of the external N load) of fixed N to the water column through recycling mechanisms. To our knowledge, our study is the first to document the simultaneous contribution of denitrification, DNRA, anammox, and TDN recycling combined with in situ measurements.

scholarly journals Bacteriocin Production: a Probiotic Trait?

2011 ◽  
Vol 78 (1) ◽  
pp. 1-6 ◽  
Author(s):  
Alleson Dobson ◽  
Paul D. Cotter ◽  
R. Paul Ross ◽  
Colin Hill
Keyword(s):  
Immune System ◽  
Microbial Communities ◽  
Bacteriocin Production ◽  
Host Immune System ◽  
Diverse Group ◽  
Probiotic Strains ◽  
Important Trait ◽  
The Impact ◽  
Selection Of

ABSTRACTBacteriocins are an abundant and diverse group of ribosomally synthesized antimicrobial peptides produced by bacteria and archaea. Traditionally, bacteriocin production has been considered an important trait in the selection of probiotic strains, but until recently, few studies have definitively demonstrated the impact of bacteriocin production on the ability of a strain to compete within complex microbial communities and/or positively influence the health of the host. Although research in this area is still in its infancy, there is intriguing evidence to suggest that bacteriocins may function in a number of ways within the gastrointestinal tract. Bacteriocins may facilitate the introduction of a producer into an established niche, directly inhibit the invasion of competing strains or pathogens, or modulate the composition of the microbiota and influence the host immune system. Here we review the role of bacteriocin production in complex microbial communities and their potential to enhance human health.

scholarly journals Role of the Microbiome in Interstitial Lung Diseases

2021 ◽  
Vol 8 ◽  
Author(s):  
Ozioma S. Chioma ◽  
Laura E. Hesse ◽  
Austin Chapman ◽  
Wonder P. Drake
Keyword(s):  
Immune Responses ◽  
Lung Disease ◽  
Microbial Communities ◽  
Lung Diseases ◽  
Interstitial Lung Diseases ◽  
Original Research ◽  
Inflammatory Conditions ◽  
Lung Health ◽  
The Impact

There are trillions of microorganisms in the human body, consisting of bacteria, viruses, fungi, and archaea; these collectively make up the microbiome. Recent studies suggest that the microbiome may serve as a biomarker for disease, a therapeutic target, or provide an explanation for pathophysiology in lung diseases. Studies describing the impact of the microorganisms found in the respiratory tract on lung health have been published and are discussed here in the context of interstitial lung diseases. Additionally, epidemiological and experimental evidence highlights the importance of cross-talk between the gut microbiota and the lungs, called the gut–lung axis. The gut-lung axis postulates that alterations in gut microbial communities may have a profound effect on lung disease. Dysbiosis in the microbial community of the gut is linked with changes in immune responses, homeostasis in the airways, and inflammatory conditions in the gastrointestinal tract itself. In this review, we summarize studies describing the role of the microbiome in interstitial lung disease and discuss the implications of these findings on the diagnosis and treatment of these diseases. This paper describes the impact of the microbial communities on the pathogenesis of lung diseases by assessing recent original research and identifying remaining gaps in knowledge.

scholarly journals Influence of native ureolytic microbial community on biocementation potential of Sporosarcina pasteurii

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Raja Murugan ◽  
G. K. Suraishkumar ◽  
Abhijit Mukherjee ◽  
Navdeep K. Dhami
Keyword(s):  
Microbial Community ◽  
Calcium Carbonate ◽  
Kinetic Analysis ◽  
Microbial Communities ◽  
Slow Rate ◽  
Carbonate Precipitation ◽  
Calcium Carbonate Precipitation ◽  
Promising Technique ◽  
Sporosarcina Pasteurii ◽  
The Impact

AbstractMicrobially induced calcium carbonate precipitation (MICP)/Biocementation has emerged as a promising technique for soil engineering applications. There are chiefly two methods by which MICP is applied for field applications including biostimulation and bioaugmentation. Although bioaugmentation strategy using efficient ureolytic biocementing culture of Sporosarcina pasteurii is widely practiced, the impact of native ureolytic microbial communities (NUMC) on CaCO3 mineralisation via S. pasteurii has not been explored. In this paper, we investigated the effect of different concentrations of NUMC on MICP kinetics and biomineral properties in the presence and absence of S. pasteurii. Kinetic analysis showed that the biocementation potential of S. pasteurii is sixfold higher than NUMC and is not significantly impacted even when the concentration of the NUMC is eight times higher. Micrographic results revealed a quick rate of CaCO3 precipitation by S. pasteurii leading to generation of smaller CaCO3 crystals (5–40 µm), while slow rate of CaCO3 precipitation by NUMC led to creation of larger CaCO3 crystals (35–100 µm). Mineralogical results showed the predominance of calcite phase in both sets. The outcome of current study is crucial for tailor-made applications of MICP.

scholarly journals The role of sediment-induced light attenuation on primary production during Hurricane Gustav (2008)

2020 ◽  
Vol 17 (20) ◽  
pp. 5043-5055
Author(s):  
Zhengchen Zang ◽  
Z. George Xue ◽  
Kehui Xu ◽  
Samuel J. Bentley ◽  
Qin Chen ◽  
...  
Keyword(s):  
Primary Production ◽  
Water Column ◽  
Chlorophyll Concentration ◽  
Light Attenuation ◽  
Sediment Concentration ◽  
Biogeochemical Model ◽  
System A ◽  
Sensitivity Tests ◽  
The Impact

Abstract. We introduced a sediment-induced light attenuation algorithm into a biogeochemical model of the Coupled Ocean–Atmosphere–Wave–Sediment Transport (COAWST) modeling system. A fully coupled ocean–atmospheric–sediment–biogeochemical simulation was carried out to assess the impact of sediment-induced light attenuation on primary production in the northern Gulf of Mexico during the passage of Hurricane Gustav in 2008. When compared with model results without sediment-induced light attenuation, our new model showed a better agreement with satellite data on both the magnitude of nearshore chlorophyll concentration and the spatial distribution of offshore bloom. When Hurricane Gustav approached, resuspended sediment shifted the inner shelf ecosystem from a nutrient-limited one to a light-limited one. Only 1 week after Hurricane Gustav's landfall, accumulated nutrients and a favorable optical environment induced a posthurricane algal bloom in the top 20 m of the water column, while the productivity in the lower water column was still light-limited due to slow-settling sediment. Corresponding with the elevated offshore NO3 flux (38.71 mmol N m−1 s−1) and decreased chlorophyll flux (43.10 mg m−1 s−1), the outer shelf posthurricane bloom should have resulted from the cross-shelf nutrient supply instead of the lateral dispersed chlorophyll. Sensitivity tests indicated that sediment light attenuation efficiency affected primary production when sediment concentration was moderately high. Model uncertainties due to colored dissolved organic matter and parameterization of sediment-induced light attenuation are also discussed.

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