Marine Microbiology Research Articles

Microbial Diversity and Nitrogen Cycling in Peat and Marine Soils: A Review

Nitrogen is an essential nutrient for living organisms in peat and marine soils, and its transformation within the soil matrix is a complex process mediated by various microbes that inhabit these ecological niches. The metabolism of nitrogen is governed by microbially mediated biogeochemical transformations, such as nitrification, anammox, and denitrification, which contribute to the assimilated pool of nitrogen and fixed nitrogen loss. One of the major challenges facing the field of peat and marine microbiology is the lack of understanding of the correlation between ecosystem-driven nitrogen transformation and microbial diversity. This is crucial because of growing concerns regarding the impacts of human-induced activities and global climate change on microbial nitrogen-cycling processes in peat and marine soils. Thus, this review aimed to provide a comprehensive overview of the current understanding of the microbial communities involved in peat and marine nitrification, anammox, and denitrification; the factors influencing the niche differentiation and distribution of the main functional components; the genes involved; and the main effects of human-induced activities and global climate change on the peat and marine nitrogen cycle. The implications of this review will facilitate an understanding of the complex mechanisms associated with ecosystem function in relation to nitrogen cycling, the role of peat and marine soils as carbon sinks, pollution remediation using naturally occurring populations of diverse microbes, and the development of policies to mitigate the effects of anthropogenic influences in peat and marine soils.

Seawater contamination by coring and pore water sampling of marine sediments

Coring of sediments with minimal physical disturbance, and sampling of pore water with minimal contamination from seawater, are critical in marine geochemistry and microbiology. Yet, sediment coring generally causes smearing of sediment down along the inside of the core liner and leaves seawater and fluid mud trapped around the core. This seawater is a source of diffusive or advective exchange of solutes with the core, which affects the chemistry of retrieved pore water. The exchange depends on the time elapsed between coring and the end of pore water extraction. The degree of seawater contamination is difficult to determine and has generally been neglected in the geochemical literature. Yet, it is possible to quantify seawater contamination due to the high millimolar concentration of sulfate in seawater and low micromolar concentration in the subsurface methanic zone, where sulfate is largely depleted. Analysis of 540 sediment cores from a global database showed that sulfate concentration data beneath the sulfate-methane transition were often truncated and stated as “0” or “0,0” mM, thereby preventing an evaluation of seawater contamination. Among the 181 sediment cores for which the mM sulfate concentrations were reported with two or three decimal places, concentrations measured in methanic sediments were up to an order of magnitude higher than the estimated in situ concentrations in gravity cores and two orders of magnitude higher in cores recovered by scientific ocean drilling. A comparison between pore water extraction by Rhizon suction samplers and by high-pressure squeezers in cores from Baltic Sea Expedition 347 of the IODP (International Ocean Discovery Program) showed no systematic difference in the degree of contamination. A comparison with a perfluorocarbon (PFC) tracer injected by IODP coring into the drilling fluid showed a seawater contamination similar to that based on sulfate in the methanic zone. In IODP cores, where the true in situ sulfate concentration is generally unknown, we calculated the theoretical sulfate concentration that corresponded to equilibrium between SO42−, Ba2+ and barite (BaSO4) to show that the equilibrium sulfate concentrations in the methanic zone are much lower than the sulfate concentrations measured in pore water samples, again indicating seawater contamination. We used a time-resolved diffusion model to calculate how contaminating seawater ions penetrate from the external liner fluid into sediment cores before pore water is extracted. We conclude that nearly all published pore water samples retrieved from subsurface sediments are contaminated by seawater to some degree. We also conclude that sensitive sulfate analyses in methanic sediments constitute a unique opportunity to quantify this contamination and thereby provide a better possibility to control it.

Metagenomic 18S rDNA reads revealed zonation of eukaryotic communities in the Yongle blue hole.

The Yongle blue hole (YBH), situated in the South China Sea, represents a compelling subject of study in marine microbiology due to its unique redox-layered microbial ecosystems. However, the diversity and ecology of microbial eukaryotes within the YBH remains underexplored. This study endeavors to bridge this gap through the application of the in situ microbial filtration and fixation (ISMIFF) device to collect 0.22-30 μm microbial samples from 21 water layers of YBH. Subsequent extraction of 18S rRNA metagenomic reads of 21 metagenomes and 10 metatranscriptomes facilitated a comprehensive analysis of community structures. Findings revealed a pronounced superiority in the diversity and richness of eukaryotic microorganisms in the oxic zone compared to its suboxic and anoxic counterparts. Notably, Dinophyceae and Maxillopoda emerged as the predominant taxa based on the analysis of the 18S rRNA reads for the V4 and V9 regions, which showed stratification In their relative abundance and suggested their potential role in the thermo-halocline boundaries and oxic-anoxic interface. Specifically, In these eukaryotic microbial communities, Dinophyceae exhibited significant abundance at 20 m (20.01%) and 105 m (26.13%) water depths, while Maxillopoda was prevalent at 40 m (22.84%), 80 m (23.19%), and 100 m (15.42%) depths. A part of these organisms, identified as larvae and protists, were likely attracted by swarming chemosynthetic bacterial prey prevailing at the thermo-halocline boundaries and oxic-anoxic interface. Furthermore, the phylogenetic relationships of the major 18S operational taxonomic units (OTUs) showed a close adjacency to known species, except for three Dinophyceae OTUs. In conclusion, this study provides critical insights into the vertical distribution and transcriptional activity of <30-μm eukaryotic microbes, shedding light on the taxonomic novelty of eukaryotic microorganisms within the semi-enclosed blue holes.

Hands-on Hypoxia: Engaging High School Educators in the science behind Marine Microbial Dynamics in Hypoxic Coastal Areas Through Field and Classroom Experiences

The University of Southern California’s (USC) Joint Educational Project’s STEM Education Programs hosted a three-day summer workshop focused on marine microbiology and coastal deoxygenation for high school educators. To increase ocean literacy in high school students from Title I schools, topical marine science research was translated into four lesson plans appropriate for classrooms that teach biology and environmental science. The lesson plans focus on how marine microbes affect and are affected by the dissolved oxygen content of seawater but covered diverse oceanography topics including microbial ecology, nutrient cycling, physical ocean dynamics, and climate change. This education framework was designed to promote and facilitate hands on discovery-based learning and making observations about the natural world. The workshop and lesson plan development were executed in partnership with faculty and graduate students researching marine microbes and oceanography from USC’s Marine and Environmental Biology department to provide scientific expertise on the subject matter. At the workshop, educators were guided through each lesson plan and given classroom sets of materials to complete each of the experiments in their own classrooms. Educators also had the opportunity to experience the academic research process at both USC and the Wrigley Institute of Environmental Studies on Catalina Island, California. Teachers valued this interactive experience to learn from professional scientists and STEM educators. They left the workshop equipped with the knowledge and confidence to teach these marine microbiology and biogeochemistry concepts in their classrooms.

A marine lipopeptides-producing Bacillus amyloliquefaciens HY2-1 with a broad-spectrum antifungal and antibacterial activity and its fermentation kinetics study.

The antagonistic Bacillus amyloliquefaciens HY2-1 was a marine microbiology that was isolated previously from the seabed silt of Beibu Gulf in China by dual culture with Penicillium digitatum. As a continuous study, the present work focused on evaluating the antimicrobial activity, identifying the produced active components, and revealing the fermentation characteristics of B. amyloliquefaciens HY2-1, respectively. It was found that B. amyloliquefaciens HY2-1 exhibited a broad-spectrum antimicrobial activity against the tested seven phytopathogenic fungi and five pathogenic bacteria by producing Bacillus lipopeptides such as fengycin A (C14 to C19 homologues) and surfactin (C14 and C15 homologues). Morphological observation of P. digitatum under light microscope, scanning electron microscopy, transmission electron microscopy, and fluorescence microscope inferred that B. amyloliquefaciens exerted the antagonistic activity by damaging the fungal cell membrane, thus inhibiting the mycelium growth and sporification of phytopathogenic fungi. As a marine microbiology, our results showed that B. amyloliquefaciens could survive and metabolize even at the culture condition with 110g/L of NaCl concentration, and the produced antimicrobial compounds exhibited excellent thermostability and acid-alkali tolerance. The dynamic models were further constructed to theoretically analyze the fermentation process of B. amyloliquefaciens HY2-1, suggesting that the synthesis of antimicrobial compounds was coupled with both cell growth and cell biomass. In conclusion, the marine lipopeptides-producing B. amyloliquefaciens HY2-1 showed a promising prospect to be explored as a biocontrol agent for plant disease control of crops and postharvest preservation of fruits and vegetables, especially due to its outstanding stress resistance and the broad-spectrum and effective antagonist on various phytopathogenic fungi.

The Landscape of Global Ocean Microbiome: From Bacterioplankton to Biofilms.

The development of metagenomics has opened up a new era in the study of marine microbiota, which play important roles in biogeochemical cycles. In recent years, the global ocean sampling expeditions have spurred this research field toward a deeper understanding of the microbial diversities and functions spanning various lifestyles, planktonic (free-living) or sessile (biofilm-associated). In this review, we deliver a comprehensive summary of marine microbiome datasets generated in global ocean expeditions conducted over the last 20 years, including the Sorcerer II GOS Expedition, the Tara Oceans project, the bioGEOTRACES project, the Micro B3 project, the Bio-GO-SHIP project, and the Marine Biofilms. These datasets have revealed unprecedented insights into the microscopic life in our oceans and led to the publication of world-leading research. We also note the progress of metatranscriptomics and metaproteomics, which are confined to local marine microbiota. Furthermore, approaches to transforming the global ocean microbiome datasets are highlighted, and the state-of-the-art techniques that can be combined with data analyses, which can present fresh perspectives on marine molecular ecology and microbiology, are proposed.

Viral infection in the ocean-A journey across scales.

Viruses are the most abundant biological entity in the ocean and infect a wide range of microbial life across bacteria, archaea, and eukaryotes. In this essay, we take a journey across several orders of magnitude in the scales of biological organization, time, and space of host-virus interactions in the ocean, aiming to shed light on their ecological relevance. We start from viruses infecting microbial host cells by delivering their genetic material in seconds across nanometer-size membranes, which highjack their host's metabolism in a few minutes to hours, leading to a profound transcriptomic and metabolic rewiring. The outcome of lytic infection leads to a release of virions and signaling molecules that can reach neighboring cells a few millimeters away, resulting in a population whose heterogeneous infection level impacts the surrounding community for days. These population dynamics can leave unique metabolic and biogeochemical fingerprints across scales of kilometers and over several decades. One of the biggest challenges in marine microbiology is to assess the impact of viruses across these scales, from the single cell to the ecosystem level. Here, we argue that the advent of new methodologies and conceptual frameworks represents an exciting time to pursue these efforts and propose a set of important challenges for the field. A better understanding of host-virus interactions across scales will inform models of global ocean ecosystem function in different climate change scenarios.

Complete Genome Sequence of Vibrio natriegens Strain PWH3a

Vibrio natriegens strain PWH3a, isolated from the Texas Gulf Coast, is used as a model organism in marine microbiology. Here, we report the complete genome sequence of strain PWH3a, which has two circular chromosomes, 4,650 coding sequences, 34 rRNA, 4 noncoding RNA (ncRNA), 131 tRNA genes, and one Mu-like prophage sequence.

Isolation of marine hydrocarbonoclastic bacteria from petroleum contaminated sites in Dumai

The Dumai Sea is vulnerable to pollution, especially oil spills. Oil pollution in Dumai seawater causes a decline in the population of aquatic organisms. Isolation and screening of marine hydrocarbonoclastic bacteria is one effort to find potential local agents. This research aims to isolate marine hydrocarbonoclastic bacteria from the Petroleum Contaminated Site in Dumai. This research uses a survey method, and it was in four stages such as, isolation, screening, morphological and physiological characteristics, bacterial identification, and data analysis. Water samples were taken using purposive sampling at seven different locations. The samples were analyzed in situ, including water characteristics, pH, temperature, salinity, and brightness. Furthermore, the water samples were further analyzed at the Marine Microbiology Laboratory, University of Riau. Isolation and screening results showed that ten isolates of marine hydrocarbonoclastic bacteria can grow in SSMS liquid media with a petroleum content of 5%. The ten isolates in sequence are DS21a, DS22b, DS42c, DS52d, DS61e, DS62f, DS63g, DS71h, DS72i and DS73j. The characterization and identification results obtained four different genera from petroleum-contaminated sites in Dumai, sequentially Micrococcus, Rhodococcus, Marinobacter, and Bacillus.

Recent methods for discovering novel bioactive metabolites, specifically antimicrobial agents, from marine-associated micro-organisms.

Marine micro-organisms are a promising source for novel natural compounds with many medical and biotechnological applications. Here, we demonstrate limitations and recent strategies for investigating the marine microbial community for novel bioactive metabolites, specifically those of antimicrobial potential. These strategies include culture-dependent methods such as modifying the standard culture media, including changing the gelling agent, dissolving vehicle, media supplementation and preparation to access a broader range of bacterial diversity from marine samples. Furthermore, we discuss strategies such as insitu cultivation, dilution-to-extinction cultivation and long-term incubation. We are presenting recent applications of culture-independent methods such as genome mining, proteomics profiling and the application of metagenomics as a novel strategy for structure confirmation in the discovery of the marine micro-organism for novel antimicrobial metabolites. We present this review as a simple guide and a helpful resource for those who seek to enter the challenging field of applied marine microbiology.

Marine environment induced failure of FRP composites used in maritime transport

Fiber reinforced polymer (FRP) composites are being extensively considered for construction of ships and marine structures. Due to harsh environmental operational conditions, failure prediction of such structures is an imperative in this industry sector. This paper presents the final results of a 2-year research of real marine environment induced changes of mechanical properties in FRP composites.Realistic environmental input parameters for structural modeling of marine structures are crucial and can be obtained by conducting tests in real sea environment for prolonged periods, as opposed to usual accelerated laboratory experiments. In this research, samples of epoxy/glass and polyester/glass with various fiber layout configurations have been submerged under the sea for periods of 6, 12 and 24 months. An analysis of mass changes, marine microbiology growth, tensile strength and morphological structures of the coupons was performed and compared with samples exposed to room environment.All samples exhibited an increase in mass due to seawater absorption and microorganism growth in the organic resins (matrix). The tensile strength loss variation through the periods of submersion showed a correlation with the fiber layout configuration. The results of optical and scanning electron microscopical investigation indicated significant matrix morphological changes primarily due to salt crystal formation and the impact of sea microorganisms embedding in and attaching to the resin.The outcome of this research will be the basis for a set of realistic input parameters for a failure analysis numerical tool currently in development that can be applied for life-time behavior predictions of marine structures.

Mechanisms Generating Dichotomies in the Life Strategies of Heterotrophic Marine Prokaryotes

Understanding the mechanisms that generate and maintain diversity in marine prokaryotic communities is one of the main challenges for contemporary marine microbiology. We here review how observational, experimental, and theoretical evidence converge on the conclusion that the marine pelagic community of heterotrophic prokaryotes consists of organisms with two main types of life strategies. We illustrate this dichotomy by SAR11 and Vibrio spp. as typical representatives of the two strategies. A theory for life strategy dichotomy exists in classical r/K-selection. We here discuss an additional dichotomy introduced by what we term S/L-selection (for Small and Large, respectively). While r/K-selection focuses on the role of environmental disturbances, steady-state models suggest that high abundance at species level should be closely related to a low trade-off between competition and defense. We summarize literature indicating that the high availability of organic C is an essential environmental factor favoring Vibrio spp. and suggest that the essence of the generalized L-strategy is to reduce the competition-predator defense trade-off by using non-limiting organic C to increase size. The “streamlining” theory that has been suggested for the S-strategist SAR11 proposes the opposite: that low trade-off is achieved by a reduction in size. We show how this apparent contradiction disappears when the basic assumptions of diffusion-limited uptake are considered. We propose a classification scheme that combines S/L and r/K-selection using the two dimensions of organic C availability and environmental disturbance. As organic C in terrestrial runoff and size of the oligotrophic oceanic gyres are both changing, habitat size for both S- and L-strategists are affected by global change. A theory capturing the main aspects of prokaryote life strategies is therefore crucial for predicting responses of the marine microbial food web to climate change and other anthropogenic influences.

1933 Arctic Expedition on the Icebreaking Steamer A. Sibiryakov: Personal Diary of the Microbiologist B. L. Isachenko

In 1933, a scientific expedition to the northern Kara Sea on the icebreaking steamer A. Sibiryakov was conducted, organized by the All-Union Arctic Institute. Among the expedition participants was the founder of Russian marine and geological microbiology, Academician B. L. Isachenko (also spelled Issatschenko), who kept a personal diary during the expedition. This article analyzes this valuable historical source that contains the descriptions of various events that occurred during the expedition and Isachenko’s opinion on these events as well as his reflections on the optimal forms of organizing Arctic expeditions. The diary also sheds light on the inner world of the scientist who found himself in the extreme working conditions. The results he obtained during the expedition lead to the conclusions about the global human impact and future immense burden on the Arctic ecosystem.

Prolonged Real Marine Environment Exposure of Composite Marine Structures

As fiber reinforced polymer (FRP) composites become ever more established construction materials in the marine industry sector the influence of the harsh environmental operational conditions and its consequence on failure prediction of such structures is an imperative. Coupons of epoxy/glass and polyester/glass with various fiber layout configurations have been submerged under the sea for prolonged periods (6 and 12 months) in order to assess the impact on mechanical behavior of the material exposed to real marine environment as opposed to the more commonly adopted artificially produced laboratory sea environment and accelerated testing. Changes in mass, marine microbiology growth, tensile strength and morphological structures were analyzed after submersion and compared with samples exposed to room environment. All coupons have shown mass increase due to seawater absorption and microorganism growth in the organic resins matrices. The dynamic and level of change in tensile strength proved to be dependent on the fiber layout configuration. Optical and scanning electron microscopical investigation performed showed significant matrix morphological changes primarily due to salt crystal formation and the impact of sea microorganisms embedding in the resin. The collected experimental data will be used to develop a more realistic environmental input parameters for structural modeling of marine structures.

Failure analysis of FRP composites exposed to real marine environment

Fiber reinforced polymer (FRP) composites find ever growing application possibilities in marine structures. Due to harsh environmental operational conditions, failure prediction of such structures is an imperative in this industry sector. For this reason, samples of epoxy/glass and polyester/glass with various fiber layout configurations have been submerged under the sea for prolonged periods (6 and 12 months). On contrary to usual accelerated laboratory experiments, these type of tests in real sea environment and for prolonged periods are rarely done. They are useful to obtain more realistic environmental input parameters for structural modeling of marine structures. Changes in mass, marine microbiology growth, tensile strength and morphological structures were analyzed after submersion and compared with samples exposed to room environment. All samples exhibited an increase in mass due to seawater absorption and microorganism growth in the organic resins used as matrix materials. The dynamic and level of decrease in tensile strength showed dependency on the fiber layout configuration. Optical and scanning electron microscopical investigation showed significant matrix morphological changes primarily due to salt crystal formation and the impact of sea microorganisms embedding in the resin. Results of this experimental work will be used as realistic input parameters for subsequent failure analysis numerical tool that can be applied for life-time behavior predictions of marine structures.

Identification and Evaluation of Safety Hazards in Laboratories of the National Shrimp Research Institute and the Effectiveness of Measures by FMEA Technique

Introduction: Safety, raising awareness, and preventing the occurrence of hazards are necessary in order to continue to improve the quality of laboratory activities, which have been recently considered by scientific, research, and industrial communities. Therefore, the present study was conducted to determine the risk factor, potential hazards, and provide practical programs in the laboratories of the Shrimp Research Institute.&#x0D; Methods: Safety hazards of eight laboratories of the National Shrimp Research Institute were evaluated during the intervention study with the Failure Mode and Effects Analysis technique. To this end, in the first phase, the team of safety experts (HSE: Health and Safety Executive), by preparing and completing safety questionnaire forms, identified the current status of safety indicators and danger points of laboratories, assessed the distance with safety indicators, and managed danger points. Based on risk severity, probability of occurrence, and probability of risk detection, the risk priority number (RPN) was calculated, prioritized, and corrective measures were proposed. In the second phase, after corrective measures, the safety questionnaire was completed again and the level of risk severity, probability of occurrence, probability of detection, risk priority number, risk number, and percentage reduction of risk priority number of the studied laboratories were calculated and analyzed.&#x0D; Results: Thirty-five hazard points were identified in the laboratories. The range of risk priority numbers ranged from RPN = 12 for the Plankton Laboratory to RPN = 210 for the Marine Microbiology Laboratories and Marine Pollutants. After control measures, the risk number of marine microbiology laboratory was reduced to 180 and marine pollutants to 120 (P &lt;0.05).&#x0D; Conclusion: The results showed that FMEA technique is appropriate in identifying the risk points, evaluating, and classifying the risks of the Iran Shrimp Research Institute laboratories and provide control strategies to eliminate or reduce the risk rate of research environments.

Isolation and Identification of Bacteria from Dumai Marine Waters that Have Potencial as Lead Bioremediation Agents

One of the harmful pollutants to human health is the heavy metal Lead (Pb). A high concentration of lead that has can accumulate in the body of living things if in a long period of time. Lead concentrations that exceed the threshold in an environment can cause damage that affects aquatic biota and other living things. This research was carried out in February-April 2021. The purpose of this study was to isolate and identify bacteria that have the potential as lead bioremediation agents from Dumai marine waters. Isolation and identification of bacteria were carried out at the Laboratory of Marine Microbiology, Department of Marine Science, Faculty of Fisheries and Marine Sciences, and the lead concentration test at the Laboratory of Chemical Testing and Analysis, Department of Chemical Engineering, Faculty of Engineering. The results of the isolation on Marine Agar media which was added with Pb acetate (Pb(CH3COO2)) obtained three bacterial isolates from Dumai sea waters, namely D1, D2, and D3. The isolate that had the best growth was isolated D1. The isolate D1 was able to reduce the highest Pb concentration from 10 ppm by 80.53%, at a concentration of 20 ppm Pb, the isolate D1 was able to reduce Pb concentration by 78.8% and at a concentration of Pb 30 ppm, isolate D1 was able to reduce Pb concentration by 77.21%.

Analysis of Indigenous Bacteria as Microplastic Degradation of Sediment in the Sea Waters of Dumai, Riau Province

Nowdays Marine pollution resulted by microplastics is a global concern. Microplastic particles have the potential to cause damage to biota. One of solution to overcome the problem of marine pollution by microplastics by applying indigenous bacteria as microplastic degradation. This study was conducted to determine the type and ability of indigenous bacteria in sediments that are able to degrade microplastics. The research was conducted from October to December 2020. Sediment sampling was conducted in Dumai Sea Waters and sample analysis was conducted at the Marine Microbiology Laboratory, Faculty of Fisheries and Marine, Riau University. Indigenous bacteria from sediments were isolated in bacterial breeding media and then tested degradation capabilities on PET plastic samples. The result of the degradation test obtained ISL8 was able to degrade the mycoplastic with a percent degradation about 7%. Molecular test of ISL8 using PCR (Polymer chain reaction) 16S rRNA method and GenBank analysis is known that ISL8 is Bacillus sp

Quantifying Microbial Activity In Situ: the Link between Cells and Cycles.

Metagenomic sequencing of environmental samples has dramatically expanded our knowledge of microbial taxonomic and metabolic diversity and suggests metabolic interdependence is widespread. However, translating these insights into knowledge of ecosystem function and, therefore, implications for local and global chemistry, remains a challenge. In this commentary, I argue that making direct measurements of microbial activity in situ is an essential step to confirm gene-based hypotheses of microbial physiology and bridge advances in microbial ecology with a predicative understanding of global chemistry and climate. Making these measurements across a range of spatial scales and experimentally manipulated conditions contributes to a process-based understanding and, therefore, more robust predictions of how activity will respond to changing environmental conditions. I discuss recent advancements in quantifying microbial activity in situ and highlight several lines of research in marine microbiology that leverage complementary genomic and isotopic methods to connect microbes and global chemistry.

АКАДЕМИК БОРИС ЛАВРЕНТЬЕВИЧ ИСАЧЕНКО (К 150-ЛЕТИЮ СО ДНЯ РОЖДЕНИЯ)

2021 marked the 150th anniversary of the eminent scientist, Academician Boris Lavrentyevich Issatchenko (1871-1948), naturalist and microbiologist, polar researcher, founder of marine and geological microbiology, organizer of scientific study and education. The article revisits his biography, discussing his central scientific achievements, and presenting select materials of an exposition dedicated to the jubilee, at the Earth Science Museum, Moscow State University.