Marine Microbial Ecology PDF

Chapitre II: Marine microbial loop BEMA 513 – Marine Microbial Ecology Faculty of Science – UL Dr Claude Daou  Introduction — The omnipresence and key role of microorganisms in the functioning of ecological systems, especially aquatic ones, make m...

Chapitre II: Marine microbial loop BEMA 513 – Marine Microbial Ecology Faculty of Science – UL Dr Claude Daou  Introduction — The omnipresence and key role of microorganisms in the functioning of ecological systems, especially aquatic ones, make microbial ecology an essential discipline. — In the pelagic aquatic environment, the work carried out in the field of microbial ecology has shown that the flows of matter and energy: — are organized not only according to the classical linear trophic pathway based on photosynthetic assimilation (phytoplankton, zooplankton, fish), — but also use the microbial loop path to form a true food web. 2 BEMA 513_ Dr DAOU_UL/FS  Introduction — The classical linear trophic pathway The structure of the food web for the aquatic systems was so considered as being established by three levels: Ø the production of organic matter (OM) by the phytoplankton, Ø its consumption (grazing) by the zooplankton (metazoan), Ø and the predation of this one by fishes. As, in this simple and linear trophic chain, the grazing was mainly as a central role, it had been identified in the aquatic system, “grazer food chain,” and the trophic chain based on the detritus “detritus food chain” 3 BEMA 513_ Dr DAOU_UL/FS 4 BEMA 513_ Dr DAOU_UL/FS  Introduction — The Microbial food web — The investigations led in the aquatic ecosystems during the last three decades allowed to show that the flows of matter and energy are not organized only according to the linear classic trophic pathway based on the photosynthetic assimilation (phytoplankton à zooplankton à fishes), — but also borrow the microbial food web formed by the very small-sized microorganisms (pico- and nanoplankton) to form a real food web. 5 BEMA 513_ Dr DAOU_UL/FS  The microbial loop 6 BEMA 513_ Dr DAOU_UL/FS  Introduction — In aquatic environment, pelagic and benthic domains are mostly contrasted and this as well in the oceans, that in lagoons or in lakes. — The pelagic ecosystems are situated between the atmosphere and the benthic zone. The coastal marine ecosystems are also the interface between the continent and the oceanic zone. — Therefore, the coastal pelagic ecosystems are the buffer zones, on the vertical plan between the air and the benthic zone and/or on the horizontal plan, between the continent and the oceanic zone. The pelagic ecosystem is, consequently, very often under the influence of the process taking place in the adjacent ecosystems (light, rain, wind, what comes from watershed, resuspension of sediments or upwelling, etc.). 7 BEMA 513_ Dr DAOU_UL/FS  The microbial loop — The microbial loop represents the microbial food web. — The pathway starts with dissolved organic matter (DOM) which makes its way through various trophic levels ultimately to the highest trophic levels. — Organisms involved in the microbial loop include : — bacteria, microflagellates, protozoa, nematodes, ciliates, phytoplankton and various other nutrient cycling bacteria. — The microbial loop is ecologically significant because it is directly involved in nutrient cycling and primary production of biomass ultimately effecting large-scale ecological functions. 8 BEMA 513_ Dr DAOU_UL/FS  The microbial loop A bacteria-eye view of the ocean's euphotic layer. Seawater is an organic matter continuum, a gel of tangled polymers with embedded strings, sheets, and bundles of fibrils and particles, including living organisms, as “hotspots.” Bacteria (red) acting on marine snow (black) or algae (green) can control sedimentation and primary productivity; diverse microniches (hotspots) can support high bacterial diversity. 9 BEMA 513_ Dr DAOU_UL/FS  The microbial loop 10 BEMA 513_ Dr DAOU_UL/FS  The microbial loop - DOM — DOM, or dissolved organic carbon, are concentrations of free organic carbon below 0.45 micrometers. — DOM consists of molecules which were once parts of living organisms such as proteins, carbohydrates lipids and nucleic acids. — This DOM is then utilized as a food source for bacteria. — Bacteria are the only organisms capable of recycling DOM making them an extremely vital component for the continuation ecosystem function. — From here, basic food web interactions take hold. All this organic matter is transferred from smaller levels to the largest levels of ecosystems. — The DOM is recycled back into the system as various organisms from all trophic levels die off and are broken down smaller and smaller. 11 BEMA 513_ Dr DAOU_UL/FS 12 BEMA 513_ Dr DAOU_UL/FS  The microbial loop — DOM is introduced into the system in many ways including excretion of waste products from aquatic organisms. — Algal exudates are an extremely important source of DOM. — Various bacteria uptake DOM as a source of energy. These bacteria are then consumed by protozoans, microbe consumers of bacteria and algae. — Zooplankton, like copepods and other organisms then feed off these protozoans and the link to the traditional food web is established. — Zooplankton are eaten by bigger organisms (shrimp) which are eaten by bigger organisms (fish) and so on down the line. 13 BEMA 513_ Dr DAOU_UL/FS 14 BEMA 513_ Dr DAOU_UL/FS  Biological Components in the Microbial Food Webs 1. Microorganisms in Pelagic Ocean and lake Ecosystems — In pelagic marine and lake ecosystems, planktonic life-style (floating) is best adapted. — Prokaryotic or eukaryotic planktonic microorganisms may be heterotrophs, mixotrophs, or autotrophs. — These microorganisms provide almost all of the biomass production and ensure a large part of the pelagic ecosystem functions. — More generally, pelagic marine and lake ecosystems are the only ecosystems where the biomass is mainly microbial. 15 BEMA 513_ Dr DAOU_UL/FS  The microbial loop The major components in the pelagic microbial food webs (Table 13.1) are presented according to the classification of Sieburth et al. (1978): BEMA 513_ Dr DAOU_UL/FS Sieburth JMCN, Smetacek V, Lenz J (1978) Pelagic ecosystem structure: heterotrophic compartments of the plankton and their 16 relationship to plankton size fractions. Limnol Oceanogr 23:1256–1263  The microbial loop 1. Femtoplankton — In addition to very small archaea and bacteria, the femtoplankton is mainly composed of virioplankton or virus-like particles (VLP) which are ubiquitous and the most abundant biological entities in aquatic environments with concentrations ranging from 104 to 108 mL-1 17 BEMA 513_ Dr DAOU_UL/FS  The microbial loop 2. Picoplankton — Picoplankton is composed of prokaryotic and eukaryotic organisms: — archaeabacteria, — heterotrophic bacteria, — picophytoplankton (cyanobacteria and eukaryotic autotrophs), — and heterotrophic picoflagellates. — The abundance of heterotrophic bacteria in pelagic marine and lake ecosystems varies from 105 to 107 mL-1 in very oligotrophic (poor in nutrients) and more eutrophic (rich in nutrients) ecosystems, respectively. 18 BEMA 513_ Dr DAOU_UL/FS  The microbial loop 2. Picoplankton - heterotrophic bacteria 19 BEMA 513_ Dr DAOU_UL/FS  The microbial loop 2. Picoplankton - heterotrophic bacteria Simplified representation of the catabolic and anabolic pathways that influence the growth of heterotrophic bacteria. a) Oxidation of organic compounds contributes to ATP's energy pool with a rate. b) At the same time, the active transport of the substrate within the cell requires energy from ATP with a rate. c) Anabolic reactions use ATP with a rate and generate a growth rate (μ). d) Maintenance consumes ATP with a rate. e) In the absence of exogenous substrate, minimum maintenance energy should be supported by degradation of biomass from endogenous metabolism (μe) which ensures 20 BEMA 513_ Dr DAOU_UL/FS ATP production with rate.  The microbial loop 2. Picoplankton — Generally, a weak seasonal variability of the heterotrophic bacteria abundance is observed with, however, a significantly higher biomass during spring development of phytoplankton. — The abundance of cyanobacteria in coastal marine environments is highly variable but is generally about 104 mL-1 : — 7–13 x 104 mL-1 in Northwestern Mediterranean Sea — can reach 17 x 104 mL-1 in Mediterranean lagoons. — The abundance of eukaryotic picoplankton as Ostreococcus tauri is approximately 103 mL-1, particularly in coastal marine environments (lagoon). 21 BEMA 513_ Dr DAOU_UL/FS  The microbial loop 2. Picoplankton — The main predators of picoplankton in marine and lake ecosystems are the heterotrophic pico- and nanoflagellates which their abundance is about 1,000 cells mL-1. 22 BEMA 513_ Dr DAOU_UL/FS  The microbial loop 3. Nanoplancton — Nanoplankton consists of phytoplankton cells and protozoo-plankton. Some examples of nano- and microplanktonic eukaryotic microorganisms in lake ecosystems. (1) Cyclotella comta (size between 8 and 40 μm), (2) Stephanodiscus astrea (10–50 μm), (3) Cyclostephanos dubius (7–20 μm), (4) Neidium sp. (30–45 μm), (5) Pinnularia mesolepta (30–60 μm), (6) Bodo caudatus (10–20 μm), (7) Distigma proteus (40–80 μm), (8) Phacus sp. (45–90 μm) 23 BEMA 513_ Dr DAOU_UL/FS  The microbial loop 3. Nanoplancton — The nanophytoplankton together with the picophytoplankton represents important components of the microbial food webs in marine and lake ecosystems. — The abundance of nanophytoplankton is generally an order of magnitude less than that of picophytoplankton. — The main nanoheterotrophic component is protozooplankton consisting essentially of flagellates and ciliates and, incidentally, of amoebae. 24 BEMA 513_ Dr DAOU_UL/FS  The microbial loop 3. Nanoplancton — Heterotrophic nanoflagellates form an abundant ubiquitous community in marine and lake ecosystems. — They are considered the main predators of picoplankton and are thus a key component of microbial food web. — This group is particularly heterogeneous both morphologically and physiologically. They are characterized by the presence of one or more flagella involving to cells movement and food capture. — These protists flagellates can be autotroph, mixotroph, or heterotroph. 25 BEMA 513_ Dr DAOU_UL/FS  The microbial loop 4. Micro- and Mesoplankton — The microphytoplankton contributes significantly to primary production in pelagic environments. — Generally, the biomass is estimated by inverted microscopy cell counts or by measuring chlorophyll (Chl) or other pigment biomarkers by HPLC. — It is very difficult to determine an average value for the phytoplankton biomass in the marine environment, while Chl a concentrations fluctuated between 0.1 and 70 μg Chl a mL-1 in coastal lagoons. 26 BEMA 513_ Dr DAOU_UL/FS  The microbial loop 5. Microscopic fungi — Recent environmental 18S-rDNA surveys of microbial eukaryotes have unveiled major infecting agents in pelagic systems, consisting primarily of the fungal order of Chytridiales (chytrids). — Chytrids are considered the earlier branch of the Eumycetes and produce motile, flagellated zoospores, characterized by a small size (2–6 μm) and a single, posterior flagellum. — They infect a wide variety of hosts, including fishes, eggs, zooplankton, algae, and other aquatic fungi but primarily freshwater phytoplankton. 27 BEMA 513_ Dr DAOU_UL/FS  The microbial loop 5. Microscopic fungi — Ecological implications are huge because parasitic chytrids can also kill their hosts, but release substrates for microbial processes, and provide nutrient-rich particles as zoospores and short fragments (from the fragmentation of filamentous inedible hosts) for the grazer food chain. 28 BEMA 513_ Dr DAOU_UL/FS  The microbial loop Functioning of microbial food web — In oceanic pelagic ecosystems, two types of food web can be distinguished: — herbivorous or classic food web — and the microbial food web. 29 BEMA 513_ Dr DAOU_UL/FS  The microbial loop Functioning of microbial food web — The herbivorous food web is dominated by microphytoplanktonic communities (notably diatoms) assuring the essential of productivity of some regions and in some periods like spring bloom. — These phytoplanktonic communities assimilate preferentially the nitrate (coming from rivers, rain, or the upwelling deep waters rich in nitrate) and are consequently involved in the new production, feeding the large size of metazooplankton and then fishes. — The settling rate of microphytoplankton and associated products (fecal pellets produce by herbivores) being high, this type of food web is responsible of strong exportation of OM outside the euphotic zone. 30 BEMA 513_ Dr DAOU_UL/FS 31 BEMA 513_ Dr DAOU_UL/FS  The microbial loop Functioning of microbial food web — The microbial food web, including the auto- and heterotrophic microorganisms, is dominated by pico- and nanoplankton communities (cyanobacteria, heterotrophic bacteria, and flagellates) and is characteristic of oligotrophic zones. — The primary production is rather based on regenerated form of nitrogen (NH4+) and so considered as regenerated production. — The sedimentation rate of particulate organic matter (POM) in oligo- trophic areas is very low; the cells do not therefore contribute significantly to export out of the euphotic zone, and the OM is recycled on site rather by protozooplankton (flagellates and ciliates) that provides the essential link between microorganisms and macroorganisms. 32 BEMA 513_ Dr DAOU_UL/FS  The microbial loop Functioning of microbial food web – the microbial loop — There is a complexity of pelagic food webs, with all existing interactions between the various components. — Dissolved organic matter (DOM) and Particulate Organic Matter (POM) play an important role in the microbial food web. — They provide food support for the development of microbial food web and derived, in part, the phytoplankton exudation, zooplankton grazing, and bacteriovory, as well as viral lysis. 33 BEMA 513_ Dr DAOU_UL/FS  The microbial loop In marine biogeochemistry, the difference between these two fractions is made in terms of size according to a methodological criterion (a Whatman® GF/F glass fiber filter, with a nominal porosity of 0.7 μm). In microbiology, all the elements that will pass through a filter with a porosity of 0.2 μm (i.e. a size equivalent to or less than 200 kDa) are considered as dissolved, and all the elements retained by this filter as particulate. Size of the continuous spectrum of organic carbon with the distinction between the particulate phase (POC> 0.2 μm) and the dissolved phase (DOC