Natural experiments and long-term monitoring are critical to understand and predict marine host–microbe ecology and evolution

Marine multicellular organisms host a diverse collection of bacteria, archaea, microbial eukaryotes, and viruses that form their microbiome. Such host-associated microbes can significantly influence the host’s physiological capacities; however, the identity and functional role(s) of key members of the microbiome (“core microbiome”) in most marine hosts coexisting in natural settings remain obscure. Also unclear is how dynamic interactions between hosts and the immense standing pool of microbial genetic variation will affect marine ecosystems’ capacity to adjust to environmental changes. Here, we argue that significantly advancing our understanding of how host-associated microbes shape marine hosts’ plastic and adaptive responses to environmental change requires (i) recognizing that individual host–microbe systems do not exist in an ecological or evolutionary vacuum and (ii) expanding the field toward long-term, multidisciplinary research on entire communities of hosts and microbes. Natural experiments, such as time-calibrated geological events associated with well-characterized environmental gradients, provide unique ecological and evolutionary contexts to address this challenge. We focus here particularly on mutualistic interactions between hosts and microbes, but note that many of the same lessons and approaches would apply to other types of interactions.

This Essay argues that in order to truly understand how marine hosts benefit from the immense diversity of microbes, we need to expand towards long-term, multi-disciplinary research focussing on few areas of the world’s ocean that we refer to as “natural experiments,” where processes can be studied at scales that far exceed those captured in laboratory experiments.     

海洋环境中难培养微生物的寡营养培养

海洋中存在着丰富的微生物资源, 但迄今为止能够在实验室培养的微生物却不到1%, 而且能够通过培养得到的环境优势种更少, 这成为当代环境微生物学研究和海洋资源开发的最大障碍。过去十多年来, 通过不断改进培养方法和检测手段, 发明了许多新颖独特的技术, 提高了培养效率。特别是通过海洋微生物的寡营养培养技术, 分离并命名了一些难培养微生物, 给予人们极大的启发。海洋微生物资源的可持续性开发和利用, 是21世纪人类发展的重要方向, 是我们研究海洋微观世界的基础, 值得微生物学界同仁的共同关注。     

Redox-Specialized Bacterioplankton Metacommunity in a Temperate Estuary

This study explored the spatiotemporal dynamics of the bacterioplankton community composition in the Gulf of Finland (easternmost sub-basin of the Baltic Sea) based on phylogenetic analysis of 16S rDNA sequences acquired from community samples via pyrosequencing. Investigations of bacterioplankton in hydrographically complex systems provide good insight into the strategies by which microbes deal with spatiotemporal hydrographic gradients, as demonstrated by our research. Many ribotypes were closely affiliated with sequences isolated from environments with similar steep physiochemical gradients and/or seasonal changes, including seasonally anoxic estuaries. Hence, one of the main conclusions of this study is that marine ecosystems where oxygen and salinity gradients co-occur can be considered a habitat for a cosmopolitan metacommunity consisting of specialized groups occupying niches universal to such environments throughout the world. These niches revolve around functional capabilities to utilize different electron receptors and donors (including trace metal and single carbon compounds). On the other hand, temporal shifts in the bacterioplankton community composition at the surface layer were mainly connected to the seasonal succession of phytoplankton and the inflow of freshwater species. We also conclude that many relatively abundant populations are indigenous and well-established in the area.     

Genome analysis of marine photosynthetic microbes and their global role

Four recently completed genome projects on marine Cyanobacteria have started the age of comparative genomics for marine microbes. Cyanobacteria are a group of photoautotrophic bacteria that have traditionally been under-represented in studies of complete genome sequences, as have microbes from the marine environment in general. The new genome information is of crucial importance to understanding their role in oceanic primary production, global carbon cycling and functioning of the biosphere. Marine microbes are a still almost untapped resource for the identification of novel beneficial metabolites and activities. The availability of an increasing number of genome sequences will eventually lead to a sustained development of marine biotechnology.     

Exploring novel bioactive compounds from marine microbes

The historical paradigm of the deep ocean as a biological 'desert' has shifted to one of a 'rainforest' owing to the isolation of many novel microbes and their associated bioactive compounds. Recently, there has been an explosion of information about novel bioactive compounds that have been isolated from marine microbes in an effort to further explore the relatively untapped marine microbes and their secondary metabolites for drug discovery. The microbes are recovered and purified from the ocean by both conventional and innovative isolation methods to obtain those previously thought to be 'uncultivable'. To overcome the difficulties and limitations associated with cultivation techniques, several DNA-based molecular methods have been developed to bypass the culture-dependent bottleneck. Bioactive compounds isolated using the above strategies have not only shown importance in biotechnological and pharmaceutical applications but have also increased our understanding of the diversity of marine microbiota, ecosystem functions and the exploitable biology.     

Selective and differential feeding on marine prokaryotes by mucous mesh feeders

Microbial mortality impacts the structure of food webs, carbon flow, and the interactions that create dynamic patterns of abundance across gradients in space and time in diverse ecosystems. In the oceans, estimates of microbial mortality by viruses, protists, and small zooplankton do not account fully for observations of loss, suggesting the existence of underappreciated mortality sources. We examined how ubiquitous mucous mesh feeders (i.e. gelatinous zooplankton) could contribute to microbial mortality in the open ocean. We coupled capture of live animals by blue-water diving to sequence-based approaches to measure the enrichment and selectivity of feeding by two coexisting mucous grazer taxa (pteropods and salps) on numerically dominant marine prokaryotes. We show that mucous mesh grazers consume a variety of marine prokaryotes and select between coexisting lineages and similar cell sizes. We show that Prochlorococcus may evade filtration more than other cells and that planktonic archaea are consumed by macrozooplanktonic grazers. Discovery of these feeding relationships identifies a new source of mortality for Earth's dominant marine microbes and alters our understanding of how top-down processes shape microbial community and function.     

New drugs from marine microbes: the tide is turning

This is a mini-review demonstrating that investigation of the genomics of marine microbes from all three domains has the potential to revolutionize the search for secondary metabolites originally thought to be the product of marine invertebrates. The basis for the review was a symposium at the 2005 Annual Meeting of the SIM covering some aspects of the potential for marine microbes to be the primary producers of such metabolites. The work reported at that symposium has been integrated into a fuller discussion of current published literature on the subject with examples drawn from bacteria, cyanophytes and fungi.Contribution No. 05-140 from the Center of Marine Biotechnology.D.J. Newman and R.T. Hill contributed equally.     

Movement of viruses between biomes

Viruses are abundant in all known ecosystems. In the present study, we tested the possibility that viruses from one biome can successfully propagate in another. Viral concentrates were prepared from different near-shore marine sites, lake water, marine sediments, and soil. The concentrates were added to microcosms containing dissolved organic matter as a food source (after filtration to allow 100-kDa particles to pass through) and a 3% (vol/vol) microbial inoculum from a marine water sample (after filtration through a 0.45-microm-pore-size filter). Virus-like particle abundances were then monitored using direct counting. Viral populations from lake water, marine sediments, and soil were able to replicate when they were incubated with the marine microbes, showing that viruses can move between different ecosystems and propagate. These results imply that viruses can laterally transfer DNA between microbes in different biomes.     

Movement of Viruses between Biomes

Viruses are abundant in all known ecosystems. In the present study, we tested the possibility that viruses from one biome can successfully propagate in another. Viral concentrates were prepared from different near-shore marine sites, lake water, marine sediments, and soil. The concentrates were added to microcosms containing dissolved organic matter as a food source (after filtration to allow 100-kDa particles to pass through) and a 3% (vol/vol) microbial inoculum from a marine water sample (after filtration through a 0.45-μm-pore-size filter). Virus-like particle abundances were then monitored using direct counting. Viral populations from lake water, marine sediments, and soil were able to replicate when they were incubated with the marine microbes, showing that viruses can move between different ecosystems and propagate. These results imply that viruses can laterally transfer DNA between microbes in different biomes.     

海洋微生物抗肿瘤天然产物研究进展

近年来,海洋微生物已成为抗肿瘤天然产物研究的热点,目前从海洋微生物中发现了大量新的抗肿瘤天然产物。文章综述了近几年从海洋微生物(海洋放线菌、真菌和细菌)中分离得到的抗肿瘤活性天然产物的研究进展。     

The chemical defense ecology of marine unicellular plankton: constraints, mechanisms, and impacts

The activities of unicellular microbes dominate the ecology of the marine environment, but the chemical signals that determine behavioral interactions are poorly known. In particular, chemical signals between microbial predators and prey contribute to food selection or avoidance and to defense, factors that probably affect trophic structure and such large-scale features as algal blooms. Using defense as an example, I consider physical constraints on the transmission of chemical information, and strategies and mechanisms that microbes might use to send chemical signals. Chemical signals in a low Re, viscosity-dominated physical environment are transferred by molecular diffusion and laminar advection, and may be perceived at nanomolar levels or lower. Events that occur on small temporal and physical scales in the "near-field" of prey are likely to play a role in cell-cell interactions. On the basis of cost-benefit optimization and the need for rapid activation, I suggest that microbial defense system strategies might be highly dynamic. These strategies include compartmented and activated reactions, utilizing both pulsed release of dissolved signals and contact-activated signals at the cell surface. Bioluminescence and extrusome discharge are two visible manifestations of rapidly activated microbial defenses that may serve as models for other chemical reactions as yet undetected due to the technical problems of measuring transient chemical gradients around single cells. As an example, I detail an algal dimethylsulfoniopropionate (DMSP) cleavage reaction that appears to deter protozoan feeding and explore it as a possible model for a rapidly activated, short-range chemical defense system. Although the exploration of chemical interactions among planktonic microbes is in its infancy, ecological models from macroorganisms provide useful hints of the complexity likely to be found.     

Diversity and biotechnological potential of the sponge-associated microbial consortia

Sponges are well known to harbor diverse microbes and represent a significant source of bioactive natural compounds derived from the marine environment. Recent studies of the microbial communities of marine sponges have uncovered previously undescribed species and an array of new chemical compounds. In contrast to natural compounds, studies on enzymes with biotechnological potential from microbes associated with sponges are rare although enzymes with novel activities that have potential medical and biotechnological applications have been identified from sponges and microbes associated with sponges. Both bacteria and fungi have been isolated from a wide range of marine sponge, but the diversity and symbiotic relationship of bacteria has been studied to a greater extent than that of fungi isolated from sponges. Molecular methods (e.g., rDNA, DGGE, and FISH) have revealed a great diversity of the unculturable bacteria and archaea. Metagenomic approaches have identified interesting metabolic pathways responsible for the production of natural compounds and may provide a new avenue to explore the microbial diversity and biotechnological potential of marine sponges. In addition, other eukaryotic organisms such as diatoms and unicellular algae from marine sponges are also being described using these molecular techniques. Many natural compounds derived from sponges are suspected to be of bacterial origin, but only a few studies have provided convincing evidence for symbiotic producers in sponges. Microbes in sponges exist in different associations with sponges including the true symbiosis. Fungi derived from marine sponges represent the single most prolific source of diverse bioactive marine fungal compounds found to date. There is a developing interest in determining the true diversity of fungi present in marine sponges and the nature of the association. Molecular methods will allow scientists to more accurately identify fungal species and determine actual diversity of sponge-associated fungi. This is especially important as greater cooperation between bacteriologists, mycologists, natural product chemists, and bioengineers is needed to provide a well-coordinated effort in studying the diversity, ecology, physiology, and association between bacteria, fungi, and other organisms present in marine sponges.     

Microbial seascapes revisited

A remarkable array of new discoveries is emerging from studies of naturally occurring marine microbes. These discoveries originate from novel applications of evolving technologies, ranging from molecular phylogenetics to stable isotope analyses, to advanced microscopic techniques, to genomics. As a consequence, new perspectives on the natural history of marine microbes, the inseparable nature of the geological and biological worlds, and a plethora of unexpected new genotypes, phenotypes and physiologies are now being revealed. As our observations of naturally occurring microbes become increasingly more sophisticated, so will theory, technical applications and predictive capabilities in microbial ecology.     

Low-salinity transitions drive abrupt microbial response to sea-level change

The salinisation of many coastal ecosystems is underway and is expected to continue into the future because of sea-level rise and storm intensification brought about by the changing climate. However, the response of soil microbes to increasing salinity conditions within coastal environments is poorly understood, despite their importance for nutrient cascading, carbon sequestration and wider ecosystem functioning. Here, we demonstrate deterioration in the productivity of a top-tier microbial group (testate amoebae) with increasing coastal salinity, which we show to be consistent across phylogenetic groups, salinity gradients, environment types and latitude. Our results show that microbial changes occur in the very early stages of marine inundation, presaging more radical changes in soil and ecosystem function and providing an early warning of coastal salinisation that could be used to improve coastal planning and adaptation.     

A metabarcoding analysis of the wrackbed microbiome indicates a phylogeographic break along the North Sea–Baltic Sea transition zone

Sandy beaches are biogeochemical hotspots that bridge marine and terrestrial ecosystems via the transfer of organic matter, such as seaweed (termed wrack). A keystone of this unique ecosystem is the microbial community, which helps to degrade wrack and re-mineralize nutrients. However, little is known about this community. Here, we characterize the wrackbed microbiome as well as the microbiome of a primary consumer, the seaweed fly Coelopa frigida, and examine how they change along one of the most studied ecological gradients in the world, the transition from the marine North Sea to the brackish Baltic Sea. We found that polysaccharide degraders dominated both microbiomes, but there were still consistent differences between wrackbed and fly samples. Furthermore, we observed a shift in both microbial communities and functionality between the North and Baltic Sea driven by changes in the frequency of different groups of known polysaccharide degraders. We hypothesize that microbes were selected for their abilities to degrade different polysaccharides corresponding to a shift in polysaccharide content in the different seaweed communities. Our results reveal the complexities of both the wrackbed microbial community, with different groups specialized to different roles, and the cascading trophic consequences of shifts in the near shore algal community.     

The microbial environment of marine deposit-feeder guts characterized via microelectrodes

Microbial viability and growth in animal guts are dependent upon conditions influenced by both the physiological activities of the animal and the activities of the microbes themselves. To examine the relative contribution of these influences, the guts of Molpadia intermedia (a subtidal holothuroid) and a variety of other marine deposit feeders from diverse habitats were probed with mini- or microelectrodes to measure oxygen, Eh, and pH. In general, bulk oxygen and pH conditions of the gut mimicked those of ambient sediments, revealing nearly neutral pH and zero oxygen in sub- and intertidal animals, with more oxygen in bathyal animals ingesting oxygenated sediments. Eh in guts of subsurface deposit feeders that likely subduct and aerate sediments before ingestion did not mimic sediments. Axial Eh profiles, in contrast to those of pH and oxygen, revealed significant changes along the gut. In most deposit feeders, values decreased from mouth to midgut, suggesting high rates of microbial metabolism within the gut. Increases in Eh were observed in the most distal portion of guts, however, likely due to anal intake of aerated water, and throughout the guts of terebellid polychaetes that feed on highly reducing sediments. This addition of a strong oxidant by the animal may be necessary to avoid sulfide poisoning and may provide access to organic products by stimulating chemoautotrophy. Radial profiles of the gut revealed sharp gradients of Eh and oxygen. In general, steep redox gradients stimulate bacterial metabolism and may lead to exceptionally high respiratory rates. Radial diffusion calculations made using oxygen profiles surrounding the gut reveal that, as predicted by digestion theory, oxygen consumption rates are rapid and are higher in the hindgut, where the digestive products of the animal are available to microbes, than in the foregut.Offprint requests to: C. Plante.     

近岸海洋线虫与细菌、古菌的共现性及其对碳、氮循环的影响

【目的】初步探究海洋线虫与微生物的相互作用对碳、氮循环的影响。【方法】利用16S r RNA和18S r RNA基因高通量测序方法,对33个近岸沉积物样品中细菌、古菌和真核生物的多样性进行调查;对海洋线虫与细菌、海洋线虫与古菌的共现性进行网络分析,并采用Spearman统计学方法,识别出与海洋线虫共现性呈显著相关性的微生物种类。【结果】在夏季,红树林和潮间带泥滩样品中线虫OTU平均相对丰度基本呈随深度增加而递减趋势;冬季的红树林样品中发现相类似变化规律,只有在冬季潮间带泥滩样品中线虫OTU平均相对丰度在深层较高于表层。相对丰度最高的海洋线虫隶属于单宫目(47%)、色矛目(19%)、刺嘴目(16%)和垫刃目(9%),它们与热源体古菌、深古菌、γ-和δ-变形菌等微生物有显著正/负相关关系。【结论】在香港米埔湿地沉积物中,与相对丰度最高的5种线虫显著相关的几大类微生物均在碳、氮、硫等元素循环方面起十分重要的作用,暗示海洋线虫与微生物潜在的相互作用对元素地球化学循环具有重要影响。研究结果有助于深入了解线虫在生态系统中未被揭示的生态功能,有助于更清晰地认识海洋线虫在底栖生态系统中所扮演的角色。     

HBMMD: an enhanced database of the microorganisms associated with deeper water marine invertebrates

The Harbor Branch Marine Microbial Database (HBMMD) provides preliminary taxonomic identifications and features of microorganisms maintained in the Harbor Branch Oceanographic Institution Marine Microbial Culture Collection. The microbes are primarily derived from marine invertebrates such as sponges (phylum Porifera) and soft corals (phylum Cnidaria) found in deep water environments [>120 feet (>35 m) seawater]. The microbes isolated from within marine invertebrates represent some unique taxa and phylogenetic signatures. The database provides a user-friendly method to systemically search or sort a desired input. The site allows a powerful search for multiple parameters of any entry. Images of the microbes are contained within the database and can be accessed from the website. The HBMMD homepage is located at .     

Flow cytometric characterization of marine microbes

The analysis of marine phytoplankton using flow cytometry has enabled the discovery of new taxa and has contributed new understanding to the dynamics and ecological contributions of phytoplankton to the global carbon cycle. Marine phytoplankton are uniquely suited to analysis by flow cytometry because of their size, pigment content, and ability to remain in suspension. Cytometric analysis of marine populations is not without challenges. Phytoplankton communities span a broad range of sizes. The smallest microbes are a few tenths of a micron, while the largest are a few tenths of a millimeter. The improvement of cytometric measurements of scattered laser light allows one to investigate marine microbes whose sizes span several orders of magnitude. To effectively leverage the advantages that marine microbes possess, cytometers have to be carefully engineered for marine use.     

Zebrafish Embryo Toxicity Microscale Model for Ichthyotoxicity Evaluation of Marine Natural Products

Marine organisms often protect themselves against their predators by chemical defensive strategy. The second metabolites isolated from marine organisms and their symbiotic microbes have been proven to play a vital role in marine chemical ecology, such as ichthyotoxicity, allelopathy, and antifouling. It is well known that the microscale models for marine chemoecology assessment are urgently needed for trace quantity of marine natural products. Zebrafish model has been widely used as a microscale model in the fields of environment ecological evaluation and drug safety evaluation, but seldom reported for marine chemoecology assessment. In this work, zebrafish embryo toxicity microscale model was established for ichthyotoxicity evaluation of marine natural products by using 24-well microplate based on zebrafish embryo. Ichthyotoxicity was evaluated by observation of multiple toxicological endpoints, including coagulation egg, death, abnormal heartbeat, no spontaneous movement, delayed hatch, and malformation of the different organs during zebrafish embryogenesis periods at 24, 48, and 72 h post-fertilization (hpf). 3,4-Dichloroaniline was used as the positive control for method validation. Subsequently, the established model was applied to test the ichthyotoxic activity of the compounds isolated from corals and their symbiotic microbes and to isolate the bioactive secondary metabolites from the gorgonian Subergorgia mollis under bioassay guidance. It was suggested that zebrafish embryo toxicity microscale model is suitable for bioassay-guided isolation and preliminary bioactivity screening of marine natural products.