The role of Bacterial-based Protist Communities in Aquatic and Soil Ecosystems and the Carbon Biogeochemical Cycle, with Emphasis on Naked Amoebae

Current research is reviewed on aquatic and soil microbial ecology with attention to the fate of organic carbon in bacterial-based protist food webs, including some new data. Particular attention is given to the effects of pulsed sources of low-molecular weight organic sources of carbon on soil respiration, changes in bacterial, nanoflagellate, and naked amoeba C-biomass, and evidence for throughput of carbon in microbial food webs in Arctic and some low-latitude, temperate soil environments. The proportion of pulsed sources of glucose-C that is sequestered in microbial biomass relative to loss as CO2 is examined in laboratory experimental studies, and implications of the research for microbial community dynamics and global warming due to terrestrial sources of respiratory CO2 are discussed

Ultrastructure of Diplophrys parva, a New Small Freshwater Species, and a Revised Analysis of Labyrinthulea (Heterokonta)

We describe Diplophrys parva n. sp., a freshwater heterotroph, using fine structural and sequence evidence. Cells are small (L = 6.5 ± 0.08, W = 5.5 ± 0.06 µm; mean ± SE) enclosed by an envelope/theca of overlapping scales, slightly oval to elongated-oval with rounded ends, (1.0 × 0.5–0.7 µm), one to several intracellular refractive granules (~ 1.0–2.0 µm), smaller hyaline peripheral vacuoles, a nucleus with central nucleolus, tubulo-cristate mitochondria, and a prominent Golgi apparatus with multiple stacked saccules (~ 10). It is smaller than published sizes of Diplophrys archeri (~ 10–20 µm), modestly less than Diplophrys marina (~ 5–9 µm), and differs in scale size and morphology from D. marina. No cysts were observed. We transfer D. marina to a new genus Amphifila as it falls within a molecular phylogenetic clade extremely distant from that including D. parva. Based on morphological and molecular phylogenetic evidence, Labyrinthulea are revised to include six new families, including Diplophryidae for Diplophrys and Amphifilidae containing Amphifila. The other new families have distinctive morphology: Oblongichytriidae and Aplanochytriidae are distinct clades on the rDNA tree, but Sorodiplophryidae and Althorniidae lack sequence data. Aplanochytriidae is in Labyrinthulida; the rest are in Thraustochytrida; Labyrinthomyxa is excluded

Experimental Evidence for Non-encysted, Freeze-resistant Stages of Terrestrial Naked Amoebae Capable of Resumed Growth after Freeze-thaw Events

Experimental evidence is presented to support a hypothesis that terrestrial naked amoebae, collected during late autumn from cold, moist temperate soil, develop a non-encysted, freeze-thaw resistant stage that is capable of surviving winter frozen soil. Therefore, in addition to cyst formation, naked amoebae may survive harsh, frozen winter soil in a dormant or resting stage that is capable of rapid resumed growth in spring, thus gaining an immediate competitive advantage in exploiting food and other environmental resources early after the winter thaw

The role of Bacterial-based Protist Communities in Aquatic and Soil Ecosystems and the Carbon Biogeochemical Cycle, with Emphasis on Naked Amoebae

Current research is reviewed on aquatic and soil microbial ecology with attention to the fate of organic carbon in bacterial-based protist food webs, including some new data. Particular attention is given to the effects of pulsed sources of low-molecular weight organic sources of carbon on soil respiration, changes in bacterial, nanoflagellate, and naked amoeba C-biomass, and evidence for throughput of carbon in microbial food webs in Arctic and some low-latitude, temperate soil environments. The proportion of pulsed sources of glucose-C that is sequestered in microbial biomass relative to loss as CO2 is examined in laboratory experimental studies, and implications of the research for microbial community dynamics and global warming due to terrestrial sources of respiratory CO2 are discussed

Soil Respiration, Climate Change and the Role of Microbial Communities

Although this contribution is not intended to be a comprehensive perspective on current knowledge of soil respiration, a brief overview of some pertinent research on global patterns of soil respiration is presented first to establish a context for the subsequent more focused discussion of the role of microbial communities in soil carbon budgets and net respiratory CO2 flux to the atmosphere. Major reviews, and relevant broad research studies of current knowledge about regional and global respiratory flux patterns, are available from other sources. These include reviews of terrestrial respiration in broad geographical regions (e.g. [Luo and Zhou, 2006] , [Peng and Apps, 2000] , [Raich and Schlesinger, 1992] , [Schimel, 1995] and [Schlesinger, 1997] ); in particular geographic regimes and biomes (e.g. [Anderson, 2010a] , [Bekku et al., 2003] , [Bond-Lamberty and Thomson, 2010] and [Townsend et al., 1992] ); and in relation to soil decomposition processes (e.g. [Adl, 2003] and [Tate, 1995] ). Calculated on a global scale, soil respiration releases carbon at a rate that is more than one order of magnitude larger than anthropogenic emissions (Luo and Zhou 2006, p. 24). With increasing evidence of global climate change, including increasing global temperature and likely major changes in patterns of precipitation, effects on soil microbial communities are likely to be significant, especially at higher latitudes where thawing of the permafrost may release substantial quantities of stored-up carbon compounds, thus increasing microbial respiration and efflux of CO2 to the atmosphere. In the final sections, discussion focuses on emerging evidence of the effects of climate change, especially changing precipitation patterns and soil moisture, on the dynamics of microbial communities and respiratory CO2 emissions. Some of the prospects and challenges for future inquiry on the role of soil microbial communities in terrestrial carbon budgets and CO2 efflux are discussed in relation to emerging research themes and new methodological approaches

Particle-associated Planktonic Naked Amoebae in the Hudson Estuary: Size-fraction Related Densities, Cell Sizes and Estimated Carbon Content

Naked amoeba densities, sizes, biodiversity and carbon content were examined in relation to two particle size fractions (< 200 μm and > 200 μm) of suspended matter in the water column of the Hudson Estuary at a near-shore location south of the Tappan Zee, Palisades, New York. The densities varied markedly among the two particle fractions, and therefore the mean densities were not significantly different between the larger and smaller particle fractions. In contrast, the mean sizes and mean carbon content were statistically greater on larger size suspended particles compared to smaller size particles. There was a broader size range of amoebae on the larger particles, including very large Cochliopodium, Vannella, Mayorella, and Hartmannella species suggesting a larger biodiversity, also indicated by a larger diversity coefficient for the > 200-μm-particle fraction compared to the < 200-μm-particle fraction, 4.51 and 4.18, respectively. In conclusion, the size of suspended particulates in the water column of near-shore, estuarine habitats may have a significant influence on the composition of naked amoebae communities and their ecological roles, especially the organization of particle-associated microbial food webs

Small pigmented eukaryotes play a major role in carbon cycling in the P‐depleted western subtropical North Atlantic, which may be supported by mixotrophy

We found that in the phosphate (PO4)‐depleted western subtropical North Atlantic Ocean, small‐sized pigmented eukaryotes (P‐Euk; < 5 μm) play a central role in the carbon (C) cycling. Although P‐Euk were only ~ 5% of the microbial phytoplankton cell abundance, they represented at least two thirds of the microbial phytoplankton C biomass and fixed more CO2 than picocyanobacteria, accounting for roughly half of the volumetric CO2 fixation by the microbial phytoplankton, or a third of the total primary production. Cell‐specific PO4 assimilation rates of P‐Euk and nonpigmented eukaryotes (NP‐Euk; < 5 μm) were generally higher than of picocyanobacteria. However, when normalized to biovolumes, picocyanobacteria assimilated roughly four times more PO4 than small eukaryotes, indicating different strategies to cope with PO4 limitation. Our results underline an imbalance in the CO2 : PO4 uptake rate ratios, which may be explained by phagotrophic predation providing mixotrophic protists with their largest source of PO4. 18S rDNA amplicon sequence analyses suggested that P‐Euk was dominated by members of green algae and dinoflagellates, the latter group commonly mixotrophic, whereas marine alveolates were the dominant NP‐Euk. Bacterivory by P‐Euk (0.9 ± 0.3 bacteria P‐Euk−1 h−1) was comparable to values previously measured in the central North Atlantic, indicating that small mixotrophic eukaryotes likely exhibit similar predatory pressure on bacteria. Interestingly, bacterivory rates were reduced when PO4 was added during experimental incubations, indicating that feeding rate by P‐Euk is regulated by PO4 availability. This may be in response to the higher cost associated with assimilating PO4 by phagocytosis compared to osmotrophy

Eukaryotic Microbial Communities Associated with Rock-­dwelling Foliose Lichens: A Functional Morphological and Microecological Analysis

Lichens are widely recognized as important examples of a fungal-algal or fungal-cyanophyte symbiosis; and in some cases they are a major food source for some animal grazers such as caribou (Rangifer tarandus), especially in the Arctic during winter. However, relatively little is known about the ecology of their co-associated bacterial and protistan communities. This is one of the first reports of an analysis of microbial communities associated with rock-dwelling foliose lichens (Flavoparmelia sp.), including a more detailed analysis of the microbial communities associated with segments of the shield-like, radially arranged lobes. Samples were taken from lichens on granite boulders beneath an oak and maple tree stand on the Lamont-Doherty Earth Observatory Campus, Palisades, N.Y. The bacteria and protist members of the lichen associated microbial communities are comparable to recently reported associations for foliose lichens growing on tree bark at the same locale, including the presence of large myxomycete plasmodial amebas, heterotrophic nanoflagellates, and naked and testate amebas. To obtain evidence of possible differences in the microecology of different portions of each radial lobe, three segments of the radial lobe in the shield-like lichen were sampled: 1) inner, more mature, central segment; 2) middle section linking the central and peripheral segments; and 3) outer, peripheral, usually broader, less closely attached segment. The mean densities (number/g) and biomasses (µg/g) of bacteria and heterotrophic nanoflagellates were highest in the older central segment and lowest in the peripheral segment of the radial lobes, especially when expressed on moist weight basis. Large myxomycete plasmodial amebas were typically located in the outermost segment of the radial lobe. The proportion of vannellid amebas (Vannella spp. and Cochliopodium spp.) were significantly more abundant in the samples of the inner lobes compared to non-vannellid amebas that were more prevalent in the outer lobes. The outer segment of the thallus lobe was typically more spongiose and absorbed more water per unit weight (based on a wet/dry-weight ratio) than the innermost segment. In general, patterns of densities and taxonomic composition of bacteria and eukaryotic microbes intergraded from the inner most segment to the outer part of each lobe – indicating a possible microecological gradient, coincident with the age-related and morphological radial gradations of the lobe. Overall, the evidence shows that the radial variation in the morphology and age-related variables of the three lobe segments may affect the microenvironment of the lobe segments and hence influence the organization of the microbial communities within each segment

C-Biomass of Bacteria, Fungi, and Protozoan Communities in Arctic Tundra Soil, Including Some Trophic Relationships

The ecology of tundra terrestrial environments has gained increasing attention due to potential major changes resulting from global warming and climate change. However, the composition of terrestrial microbial communities and their role in the biogeochemical carbon cycle are less well studied. This is the first report of the C-biomass of bacteria, fungi, and representative protozoa (heterotrophic nanoflagellates, naked amoebae, and testate amoebae) in Alaskan tundra soil samples, and the effects of glucose solution enrichment in laboratory studies simulating release of soluble organic compounds as may occur during permafrost melt and increased plant root exudates due to global warming. The data for three moss-rich surface samples, two in spring and one in summer (2011), are reported for C-supplemented (8,000 μg glucose-C) and non-supplemented treatments in laboratory culture. Seven days after supplementation, fungal C-biomass in the glucose-treated and untreated samples were similar in the range of 5 to 11 mg g–1 soil dry weight, the highest values in the summer samples. The bacterial C-biomass was the next highest in the range of 20 to 120 μg g–1 soil dry weight, followed by heterotrophic nanoflagellates (2 to 14 μg g–1 soil dry weight). The naked amoebae (0.13 to 0.94 μg C g–1 soil dry weight) and testate amoebae (2 to 20 ng C g–1 soil dry weight) contributed the least C-biomass. All of the bacterial and protozoan treatments showed increased biomass with glucose supplementation. Based on size, and C-biomass estimates, the phagotrophic protozoa appear to be organized in a classical bacterial-based trophic hierarchy (i.e. bacteria – nanoflagellates – naked amoebae – testate amoebae, in ascending order). Correlations of the C-biomass of bacteria to each of the protozoa, provided further evidence of a trophic pyramid; bacteria vs. nanoflagellates (r = –0.986), indicating top-down control by predatory flagellates, bacteria vs. naked amoebae (r = –0.361) and bacteria vs. testate amoebae (r = –0.131), each of decreasing magnitude as would be predicted for higher level consumers. Estimates of bacterial predation indicated strong predatory pressures on bacteria by the protozoa, greater with C-supplementation compared to the non-supplemented treatments