Impact of Nitrate on the Structure and Function of Bacterial Biofilm Communities in Pipelines Used for Injection of Seawater into Oil Fields

ABSTRACT We studied the impact of NO3 − on the bacterial community composition, diversity, and function in in situ industrial, anaerobic biofilms by combining microsensor profiling, 15N and 35S labeling, and 16S rRNA gene-based fingerprinting. Biofilms were grown on carbon steel coupons within a system designed to treat seawater for injection into an oil field for pressurized oil recovery. NO3 − was added to the seawater in an attempt to prevent bacterial H2S generation and microbially influenced corrosion in the field. Microprofiling of nitrogen compounds and redox potential inside the biofilms showed that the zone of highest metabolic activity was located close to the metal surface, correlating with a high bacterial abundance in this zone. Upon addition, NO3 − was mainly reduced to NO2 −. In biofilms grown in the absence of NO3 −, redox potentials of <−450 mV at the metal surface suggested the release of Fe2+. NO3 − addition to previously untreated biofilms induced a decline (65%) in bacterial species richness, with Methylophaga- and Colwellia-related sequences having the highest number of obtained clones in the clone library. In contrast, no changes in community composition and potential NO3 − reduction occurred upon subsequent withdrawal of NO3 −. Active sulfate reduction was below detection levels in all biofilms, but S isotope fractionation analysis of sulfide deposits suggested that it must have occurred either at low rates or episodically. Scanning electron microscopy revealed that pitting corrosion occurred on all coupons, independent of the treatment. However, uniform corrosion was clearly mitigated by NO3 − addition.

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Dichotomy between regulation of coral bacterial communities and calcification physiology under ocean acidification conditions

Applied and Environmental Microbiology ◽

10.1128/aem.02189-20 ◽

2021 ◽

Author(s):

A. Shore ◽

R. D. Day ◽

J. A. Stewart ◽

C.A. Burge

Keyword(s):

Ocean Acidification ◽

Bacterial Communities ◽

16S Rrna Gene Sequencing ◽

Ph Gradient ◽

Rrna Gene ◽

Seawater Ph ◽

Coral Health ◽

And Function ◽

The Impact

Ocean acidification (OA) threatens the growth and function of coral reef ecosystems. A key component to coral health is the microbiome, but little is known about the impact of OA on coral microbiomes. A submarine CO2 vent at Maug Island in the Northern Marianas Islands provides a natural pH gradient to investigate coral responses to long-term OA conditions. Three coral species (Pocillopora eydouxi, Porites lobata, and Porites rus) were sampled from three sites where mean seawater pH is 8.04, 7.98, and 7.94. We characterized coral bacterial communities (using 16S rRNA gene sequencing) and determined pH of the extracellular calcifying fluid (ECF) (using skeletal boron isotopes) across the seawater pH gradient. Bacterial communities of both Porites species stabilized (decreases in community dispersion) with decreased seawater pH, coupled with large increases in the abundance of Endozoicomonas, an endosymbiont. P. lobata experienced a significant decrease in ECF pH near the vent, whereas P. rus experienced a trending decrease in ECF pH near the vent. By contrast, Pocillopora exhibited bacterial community destabilization (increases in community dispersion), with significant decreases in Endozoicomonas abundance, while its ECF pH remained unchanged across the pH gradient. Our study shows that OA has multiple consequences on Endozoicomonas abundance and suggests that Endozoicomonas abundance may be an indicator of coral response to OA. We reveal an interesting dichotomy between two facets of coral physiology (regulation of bacterial communities and regulation of calcification), highlighting the importance of multidisciplinary approaches to understanding coral health and function in a changing ocean. IMPORTANCE Ocean acidification (OA) is a consequence of anthropogenic CO2 emissions that is negatively impacting marine ecosystems such as coral reefs. OA affects many aspects of coral physiology, including growth (i.e. calcification) and disrupting associated bacterial communities. Coral-associated bacteria are important for host health, but it remains unclear how coral-associated bacterial communities will respond to future OA conditions. We document changes in coral-associated bacterial communities and changes to calcification physiology with long-term exposure to decreases in seawater pH that are environmentally relevant under mid-range IPCC emission scenarios (0.1 pH units). We also find species-specific responses that may reflect different responses to long-term OA. In Pocillopora, calcification physiology was highly regulated despite changing seawater conditions. In Porites spp., changes in bacterial communities do not reflect a breakdown of coral-bacterial symbiosis. Insights into calcification and host-microbe interactions are critical to predicting the health and function of different coral taxa to future OA conditions.

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Microbial communities associated with sediments and polymetallic nodules of the Peru Basin

10.5194/bg-2020-11 ◽

2020 ◽

Cited By ~ 1

Author(s):

Massimiliano Molari ◽

Felix Janssen ◽

Tobias Vonnahme ◽

Frank Wenzhöfer ◽

Antje Boetius

Keyword(s):

Community Composition ◽

Deep Sea ◽

Microbial Community Composition ◽

Rrna Gene ◽

Operational Taxonomic Units ◽

Polymetallic Nodules ◽

Relevant Role ◽

Bacterial And Archaeal Communities ◽

Clarion Clipperton Fracture Zone ◽

And Function

Abstract. Industrial-scale mining of deep-sea polymetallic nodules will need to remove nodules in large areas of the seafloor. The regrowth of the nodules by metal precipitation is estimated to take millions of years. Thus for future mining impact studies, it is crucial to understand the role of nodules in shaping microbial diversity and function in deep-sea environments. Here we investigated microbial community composition based on 16S rRNA gene sequences retrieved from sediments and nodules of the Peru Basin (> 4100 m water depth). The nodule field of the Peru Basin showed a typical deep-sea microbiome, with dominance of the classes Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, and Acidimicrobiia. Nodules and sediments host distinct bacterial and archaeal communities, with nodules showing lower diversity and a higher proportion of sequences related to potential metal-cycling bacteria (i.e. Magnetospiraceae, Hyphomicrobiaceae), bacterial and archaeal nitrifiers (i.e. AqS1, unclassified Nitrosomonadaceae, Nitrosopumilus, Nitrospina, Nitrospira), and bacterial sequences found in ocean crust, nodules, hydrothermal deposits and sessile fauna. Sediment and nodule communities overall shared a low proportion of Operational Taxonomic Units (OTU; 21 % for Bacteria and 19 % for Archaea). Our results show that nodules represent a specific ecological niche (i.e. hard substrate, high metal concentrations and sessile fauna), with a potentially relevant role in organic carbon degradation. Differences in nodule community composition (e.g. Mn-cycling bacteria, nitrifiers) between the Clarion-Clipperton Fracture Zone (CCZ) and the Peru Basin suggest that changes in environmental setting (i.e. sedimentation rates) play also a significant role in structuring the nodule microbiome.

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Thermal discharge-induced seawater warming alters richness, community composition and interactions of bacterioplankton assemblages in a coastal ecosystem

Scientific Reports ◽

10.1038/s41598-021-96969-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Meora Rajeev ◽

T. J. Sushmitha ◽

Chairmandurai Aravindraja ◽

Subba Rao Toleti ◽

Shunmugiah Karutha Pandian

Keyword(s):

Community Composition ◽

Species Interactions ◽

Global Climate ◽

Relative Proportion ◽

Seawater Temperature ◽

Rrna Gene ◽

Marine Microorganisms ◽

Thermal Discharge ◽

Marine Bacterioplankton ◽

The Impact

AbstractDespite accumulating evidence on the impact of global climate warming on marine microbes, how increasing seawater temperature influences the marine bacterioplankton communities is elusive. As temperature gradient created by thermal discharges provides a suitable in situ model to study the influence of warming on marine microorganisms, surface seawater were sampled consecutively for one year (September-2016 to August-2017) from the control (unimpacted) and thermal discharge-impacted areas of a coastal power plant, located in India. The bacterioplankton community differences between control (n = 16) and thermal discharge-impacted (n = 26) areas, as investigated using 16S rRNA gene tag sequencing revealed reduced richness and varied community composition at thermal discharge-impacted areas. The relative proportion of Proteobacteria was found to be higher (average ~ 15%) while, Bacteroidetes was lower (average ~ 10%) at thermal discharge-impacted areas. Intriguingly, thermal discharge-impacted areas were overrepresented by several potential pathogenic bacterial genera (e.g. Pseudomonas, Acinetobacter, Sulfitobacter, Vibrio) and other native marine genera (e.g. Marinobacter, Pseudoalteromonas, Alteromonas, Pseudidiomarina, Halomonas). Further, co-occurrence networks demonstrated that complexity and connectivity of networks were altered in warming condition. Altogether, results indicated that increasing temperature has a profound impact on marine bacterioplankton richness, community composition, and inter-species interactions. Our findings are immensely important in forecasting the consequences of future climate changes especially, ocean warming on marine microbiota.

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Marine cyanolichens from different littoral zones are associated with distinct bacterial communities

PeerJ ◽

10.7717/peerj.5208 ◽

2018 ◽

Vol 6 ◽

pp. e5208 ◽

Cited By ~ 6

Author(s):

Nyree J. West ◽

Delphine Parrot ◽

Claire Fayet ◽

Martin Grube ◽

Sophie Tomasi ◽

...

Keyword(s):

Bacterial Communities ◽

Littoral Zone ◽

Resistant Bacteria ◽

Rrna Gene ◽

Moderately Thermophilic ◽

Culture Independent ◽

Radiation Resistant ◽

Bacteroidetes Phylum ◽

And Function ◽

The Impact

The microbial diversity and function of terrestrial lichens have been well studied, but knowledge about the non-photosynthetic bacteria associated with marine lichens is still scarce. 16S rRNA gene Illumina sequencing was used to assess the culture-independent bacterial diversity in the strictly marine cyanolichen speciesLichina pygmaeaandLichina confinis, and the maritime chlorolichen speciesXanthoria aureolawhich occupy different areas on the littoral zone. Inland terrestrial cyanolichens from Austria were also analysed as for the marine lichens to examine further the impact of habitat/lichen species on the associated bacterial communities. TheL. confinisandL. pygmaeacommunities were significantly different from those of the maritimeXanthoria aureolalichen found higher up on the littoral zone and these latter communities were more similar to those of the inland terrestrial lichens. The strictly marine lichens were dominated by the Bacteroidetes phylum accounting for 50% of the sequences, whereas Alphaproteobacteria, notablySphingomonas, dominated the maritime and the inland terrestrial lichens. Bacterial communities associated with the twoLichinaspecies were significantly different sharing only 33 core OTUs, half of which were affiliated to the Bacteroidetes generaRubricoccus,TunicatimonasandLewinella, suggesting an important role of these species in the marineLichinalichen symbiosis. Marine cyanolichens showed a higher abundance of OTUs likely affiliated to moderately thermophilic and/or radiation resistant bacteria belonging to the Phyla Chloroflexi, Thermi, and the families Rhodothermaceae and Rubrobacteraceae when compared to those of inland terrestrial lichens. This most likely reflects the exposed and highly variable conditions to which they are subjected daily.

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Investigating colonization patterns of the infant gut microbiome during the introduction of solid food and weaning from breastmilk: A cohort study protocol

PLoS ONE ◽

10.1371/journal.pone.0248924 ◽

2021 ◽

Vol 16 (4) ◽

pp. e0248924

Author(s):

Sara Dizzell ◽

Jennifer C. Stearns ◽

Jenifer Li ◽

Niels van Best ◽

Liene Bervoets ◽

...

Keyword(s):

Gut Microbiome ◽

Infant Nutrition ◽

Solid Food ◽

Gene Profiling ◽

Rrna Gene ◽

Birth Cohorts ◽

Solid Foods ◽

Infancy And Early Childhood ◽

And Function ◽

The Impact

The first exposures to microbes occur during infancy and it is suggested that this initial colonization influences the adult microbiota composition. Despite the important role that the gut microbiome may have in health outcomes later in life, the factors that influence its development during infancy and early childhood have not been characterized fully. Guidelines about the introduction of solid foods and cessation of breastfeeding, which is thought to have a significant role in the transition to a more adult-like microbiota, are not based on microbiome research. There is even less understanding of approaches used to transition to solid food in the preterm population. The purpose of this study is to identify the impact of early life dietary events on gut microbiome community structures and function among infants born at term and pre-term. We plan to prospectively monitor the gut microbiome of infants during two critical timepoints in microbial development: the introduction of solid foods and cessation from breastmilk. A total of 35 participants from three primary observational birth cohorts (two full-term cohorts and one pre-term cohort) will be enrolled in this sub-study. Participants will be asked to collect stool samples and fill out a study diary before, during and after the introduction of solids and again during weaning from breastmilk. We will use frequent fecal sampling analyzed using 16S rRNA gene profiling, metagenomics, metabolomics, and targeted bacterial culturing to identify and characterize the microbial communities, as well as provide insight into the phenotypic characteristics and functional capabilities of the microbes present during these transitional periods of infancy. This study will provide a comprehensive approach to detailing the effects of dietary transition from breastmilk to a more adult-like solid food diet on the microbiome and in doing so will contribute to evidence-based infant nutrition guidance.

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The impact of persistent bacterial bronchitis on the pulmonary microbiome of children

10.1101/181982 ◽

2017 ◽

Author(s):

Leah Cuthbertson ◽

Vanessa Craven ◽

Lynne Bingle ◽

William O.C.M. Cookson ◽

Mark L. Everard ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Bacterial Diversity ◽

Community Composition ◽

Bacterial Communities ◽

Microbial Community Analysis ◽

Rrna Gene ◽

Healthy Children ◽

Significant Difference ◽

The Impact

AbstractPersistent bacterial bronchitis is a leading cause of chronic wet cough in young children. This study aimed to characterise the respiratory bacterial microbiota of healthy children and to assess the impact of the changes associated with the development of persistent bacterial bronchitis.Blind, protected brushings were obtained from 20 healthy controls and 24 children with persistent bacterial bronchitis, with an additional directed sample obtained from persistent bacterial bronchitis patients. DNA was extracted, quantified using a 16S rRNA gene quantitative PCR assay prior to microbial community analysis by 16S rRNA gene sequencing.No significant difference in bacterial diversity or community composition (R2 = 0.01, P = 0.36) was observed between paired blind and non-blind brushes, showing that blind brushings are a valid means of accessing the airway microbiota. This has important implications for collecting lower respiratory samples from healthy children. A significant decrease in bacterial diversity (P < 0.001) and change in community composition (R2 = 0.08, P = 0.004) was observed between controls and patients. Bacterial communities within patients with PBB were dominated by Proteobacteria, and indicator species analysis showed that Haemophilus and Neisseria were significantly associated with the patient group. In 15 (52.9%) cases the dominant organism by sequencing was not identified by standard routine clinical culture.The bacteria present in the lungs of patients with persistent bacterial bronchitis were less diverse in terms of richness and evenness. The results validate the clinical diagnosis, and suggest that more attention to bacterial communities in children with chronic cough may lead to more rapid recognition of this condition with earlier treatment and reduction in disease burden.

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The Effects of Earthworms on Fungal Diversity and Community Structure in Farmland Soil With Returned Straw

Frontiers in Microbiology ◽

10.3389/fmicb.2020.594265 ◽

2020 ◽

Vol 11 ◽

Author(s):

Ke Song ◽

Yafei Sun ◽

Qin Qin ◽

Lijuan Sun ◽

Xianqing Zheng ◽

...

Keyword(s):

Community Structure ◽

Soil Carbon ◽

Community Composition ◽

Fungal Community ◽

Rrna Gene ◽

Evolutionary Analysis ◽

Α Diversity ◽

Farmland Soil ◽

Straw Return ◽

The Impact

BackgroundTo promote the decomposition of returned straw, reduce the incidence of soil-borne diseases caused by returned straw, and accelerate the conversion of straw carbon into soil carbon, we inoculated earthworms into fields with returned straw. The earthworms accelerated straw degradation and promoted carbon conversion. However, the impact of externally inoculated earthworms on the farmland soil ecosystem, especially the structure and the function of its microbial community, remains unclear.MethodsWe analyzed the effects of straw return and earthworms on the diversity of fungal populations and the community structure of dominant fungal taxa in soil by quantifying fungal population size and community composition via PCR amplification of internal transcribed spacer genes and 18S rRNA gene sequencing.ResultsThe results showed that earthworm inoculation significantly accelerated the degradation of rice straw and promoted the conversion of straw carbon to soil carbon. Both fungal abundance and α-diversity (Sobs and Shannon indices) were higher in the plots with surface straw but without earthworms than in those inoculated with earthworms and in the CK. Principal component analysis indicated that straw return increased the diversity and the abundance of the fungal community, whereas earthworms inhibited this expansion of the fungal community caused by straw return. Interestingly, the overall differences in fungal community composition were smallest in plots with straw return, while the dominant fungal community features in plots inoculated with earthworms were closer to those of the CK.ConclusionGenerally, straw return stimulated unclassified_K_fungi, Pseudeurotium, and Fusarium with strong cellulolytic ability. In contrast, the abundances of Stachybotrys, unclassified_c_Sordariomycetes, unclassified_f_Lasiosphaeriaceae, and Schizothecium were higher in the plots inoculated with earthworms and in the CK. Furthermore, evolutionary analysis showed that the evolution of soil fungal communities tended to diverge after straw return, and the evolutionary directions of fungal species in the plots inoculated with earthworms were similar to those in the CK.

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Marine cyanolichens from different littoral zones are associated with distinct bacterial communities

10.1101/209320 ◽

2017 ◽

Author(s):

Nyree J. West ◽

Delphine Parrot ◽

Claire Fayet ◽

Martin Grube ◽

Sophie Tomasi ◽

...

Keyword(s):

Bacterial Communities ◽

Littoral Zone ◽

Resistant Bacteria ◽

Rrna Gene ◽

Moderately Thermophilic ◽

Culture Independent ◽

Radiation Resistant ◽

Bacteroidetes Phylum ◽

And Function ◽

The Impact

AbstractThe microbial diversity and function of terrestrial lichens has been well studied, but knowledge about the non-photosynthetic bacteria associated with marine lichens is still scarce. 16S rRNA gene Illumina sequencing was used to assess the culture-independent bacterial diversity in the strictly marine cyanolichen speciesLichina pygmaeaandLichina confinis, and the maritime chlorolichen speciesXanthoria aureolawhich occupy different areas on the littoral zone. Inland terrestrial cyanolichens from Austria were also analysed as for the marine lichens to examine further the impact of habitat/lichen species on the associated bacterial communities. TheL. confinisandL. pygmaeacommunities were significantly different from those of the maritimeXanthoria aureolalichen found higher up on the littoral zone and these latter communities were more similar to those of the inland terrestrial lichens. The strictly marine lichens were dominated by the Bacteroidetes phylum accounting for 50% of the sequences, whereas Alphaproteobacteria, notablySphingomonas, dominated the maritime and the inland terrestrial lichens. Bacterial communities associated with the twoLichinaspecies were significantly different sharing only 33 core OTUs, half of which were affiliated to the Bacteroidetes generaRubricoccus, TunicatimonasandLewinella, suggesting an important role of these species in the marineLichinalichen symbiosis. Marine cyanolichens showed a higher abundance of OTUs likely affiliated to moderately thermophilic and/or radiation resistant bacteria belonging to the Phyla Chloroflexi, Thermi, and the families Rhodothermaceae and Rubrobacteraceae when compared to those of inland terrestrial lichens. This most likely reflects the exposed and highly variable conditions to which they are subjected daily.

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Minor impacts of reduced pH on bacterial biofilms on settlement tiles along natural pH gradients at two CO2 seeps in Papua New Guinea

ICES Journal of Marine Science ◽

10.1093/icesjms/fsw204 ◽

2017 ◽

Vol 74 (4) ◽

pp. 978-987 ◽

Cited By ~ 6

Author(s):

Christiane Hassenrück ◽

Halina E. Tegetmeyer ◽

Alban Ramette ◽

Katharina E. Fabricius

Keyword(s):

Coral Reefs ◽

Papua New Guinea ◽

Community Composition ◽

Light Exposure ◽

New Guinea ◽

Bacterial Biofilm ◽

Bacterial Biofilms ◽

Rrna Gene ◽

Strong Impact ◽

Ph Gradients

Bacterial biofilms provide cues for the settlement of marine invertebrates such as coral larvae, and are therefore important for the resilience and recovery of coral reefs. This study aimed to better understand how ocean acidification may affect the community composition and diversity of bacterial biofilms on surfaces under naturally reduced pH conditions. Settlement tiles were deployed at coral reefs in Papua New Guinea along pH gradients created by two CO2 seeps. Biofilms on upper and lower tiles surfaces were sampled 5 and 13 months after deployment. Automated Ribosomal Intergenic Spacer Analysis was used to characterize 240 separate bacterial communities, complemented by amplicon sequencing of the bacterial 16S rRNA gene of 16 samples. Bacterial biofilms consisted predominantly of Alpha-, Gamma-, and Delta-proteobacteria, as well as Cyanobacteria, Flavobacteriia, and Cytophagia, whereas taxa that induce settlement of invertebrate larvae only accounted for a small fraction of the community. Bacterial biofilm composition was heterogeneous, with on average only ∼25% of operational taxonomic units shared between samples. Among the observed environmental parameters, pH was only weakly related to community composition (R2 ∼ 1%), and was unrelated to community richness and evenness. In contrast, biofilms strongly differed between upper and lower tile surfaces (contrasting in light exposure and grazing intensity). There also appeared to be a strong interaction between bacterial biofilm composition and the macroscopic components of the tile community. Our results suggest that on mature settlement surfaces in situ, pH does not have a strong impact on the composition of bacterial biofilms. Other abiotic and biotic factors such as light exposure and interactions with other organisms may be more important in shaping bacterial biofilms on mature surfaces than changes in seawater pH.

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Mutual environmental drivers of the community composition, functional attributes and co-occurrence patterns of bacterioplankton in the composite aquatic ecosystem of Taihu watershed in China

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa137 ◽

2020 ◽

Vol 96 (8) ◽

Author(s):

Mingkun Liu ◽

Xue Han ◽

Jun Tong ◽

Huifeng Zhu ◽

Xiaohui Bai

Keyword(s):

Community Composition ◽

Relative Abundance ◽

Environmental Drivers ◽

Environmental Predictors ◽

Anthropogenic Contamination ◽

Bacterioplankton Community ◽

Functional Attributes ◽

And Function ◽

Occurrence Patterns ◽

The Impact

ABSTRACT This study aimed to determine the environmental and ecological factors influencing the planktonic prokaryotic community profiles in the composite ecosystem comprising Taihu Lake, Taipu River and Jinze Reservoir in the Taihu Watershed in China. A total of 42 water samples were intermittently collected from different sites in 6 months across four seasons. Physicochemical characteristics of the ecosystem, bacterioplankton diversity and composition, the presence of co-occurrence patterns, and environmental predictors of ecological modules in the bacterioplankton network were determined. The central species played a more important role in regulating the structure and function of the bacterioplankton community and in responding to environmental contamination than the entire community. The relative abundance of the phylum Proteobacteria and the class Betaproteobacteria varied significantly between months and locations, which were identified as core functional taxa. A non-random co-occurrence pattern and function-driven modular structure were observed in the bacterioplankton co-occurrence network. Dissolved oxygen and ammonium nitrogen were the major and mutual environmental predictors of the bacterioplankton community composition, functional attributes and relative abundance of ecological modules. The results improve our understanding of the impact of anthropogenic contamination on bacterioplankton diversity and biogeochemical cycles and the formulation of strategies for bioremediation of the Taihu Watershed.

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