Linking species and ecosystems is currently one of the great challenges in ecology. To this end, we assess here the contributions of bacteria, fungi, and detritivorous invertebrates (shredders) to leaf litter breakdown, a key ecosystem-level process. We enclosed alder (Alnus glutinosa) and willow (Salix fragilis) leaves in coarse-mesh bags (5 g dry mass), placed them in a stream during peak leaf fall, and retrieved them periodically to determine leaf mass remaining and the biomass of leaf-associated organisms. Shredder biomass was derived from numbers and length–mass relationships, bacterial numbers and biomass were determined by epifluorescence microscopy, and fungal biomass was measured as ergosterol. In addition, conidial production of aquatic hyphomycetes was determined. Leaves decomposed rapidly with exponential breakdown coefficients k of 0.035 d−1 (alder) and 0.027 d−1 (willow). Leaves were also quickly colonized within the first 4 wk of decomposition, when shredder biomass reached 263 and 141 mg d...

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Contribution of stream detrivores, fungi, and bacteria to leaf breakdown based on biomass estimates

Although prokaryotes are small in size, they are a significant biomass component in aquatic planktonic ecosystems and play a major role in biogeochemical processes. A review of the recent literature shows that the relative importance of prokaryotes to material and energy fluxes is maximized in low-productivity (oligotrophic) ecosystems and decreases in high-productivity (eutrophic) ecosystems. We conclude that competition with eukaryotic autotrophs for dissolved nutrients and competition with phagotrophic heterotrophs and physical processes (sinking, photooxidation) for organic carbon (C) play important roles in determining the relative abundance and impact of prokaryotes in aquatic systems. Oligotrophic systems have low nutrient concentrations, with high proportions of dissolved nutrients in organic form, which favors prokaryotic heterotrophs over phytoplankton. Furthermore, a high proportion of the available organic C is dissolved rather than particulate, which favors prokaryotic heterotrophs over phagotrophic heterotrophs. In eutrophic systems, increased relative concentrations and loading of inorganic nutrients and increased relative concentrations of particulate organic C select for phytoplankton and phagotrophic heterotrophs over prokaryotic heterotrophs. Increased particle sinking fluxes and/or decreased excretion of organic carbon (EOC) may also decrease the relative importance of prokaryotic heterotrophs in eutrophic systems. In oligotrophic systems, interactions between autotrophs and heterotrophs are tightly coupled because the dominant heterotrophs are similar in size and growth rates, as well as having similar nutrient composition to the dominant autotrophs, small phytoplankton. In eutrophic systems, increased productivity passes through zooplankton that are larger and have slower growth rates than the autotrophs, leading to a greater potential for decoupled auto- and heterotrophic production and increased export production.

http://www.foodweb.uhh.hawaii.edu/MARE444_files/Cotner%20&%20Biddanda%202002.pdf

Small Players, Large Role: Microbial Influence on Biogeochemical Processes in Pelagic Aquatic Ecosystems

The human gut microbiota supplies its host with essential nutrients, including B-vitamins. Using the PubSEED platform, we systematically assessed the genomes of 256 common human gut bacteria for the presence of biosynthesis pathways for eight B-vitamins: biotin, cobalamin, folate, niacin, pantothenate, pyridoxine, riboflavin, and thiamin. On the basis of the presence and absence of genome annotations, we predicted that each of the eight vitamins was produced by 40-65% of the 256 human gut microbes. The distribution of synthesis pathways was diverse; some genomes had all eight biosynthesis pathways, whereas others contained no de novo synthesis pathways. We compared our predictions to experimental data from 16 organisms and found 88% of our predictions to be in agreement with published data. In addition, we identified several pairs of organisms whose vitamin synthesis pathway pattern complemented those of other organisms. This analysis suggests that human gut bacteria actively exchange B-vitamins among each other, thereby enabling the survival of organisms that do not synthesize any of these essential cofactors. This result indicates the co-evolution of the gut microbes in the human gut environment. Our work presents the first comprehensive assessment of the B-vitamin synthesis capabilities of the human gut microbiota. We propose that in addition to diet, the gut microbiota is an important source of B-vitamins, and that changes in the gut microbiota composition can severely affect our dietary B-vitamin requirements.

/pdf/systematic-genome-assessment-of-b-vitamin-biosynthesis-o0uwsp3jyj.pdf

Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes.

It is well known that the atmosphere is a conveyor of microorganisms, and that bacteria can act as ice or cloud condensation nuclei, but clouds have not been considered as a site where organisms can live and reproduce. Here we show that bacteria in cloud droplets collected at high altitudes are actively growing and reproducing at temperatures at or below 0°C. Since ∼60% of the earth surface is covered by clouds, cloud water should be considered as a microbial habitat.

https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2000GL011684

Bacterial growth in supercooled cloud droplets

Systems biology modeling typically requires quantitative experimental data such as intracellular concentrations or copy numbers per cell. In order to convert population-averaging omics measurement data to intracellular concentrations or cellular copy numbers, the total cell volume and number of cells in a sample need to be known. Unfortunately, even for the often studied model bacterium Escherichia coli this information is hardly available and furthermore, certain measures (e.g. cell volume) are also dependent on the growth condition. In this work, we have determined these basic data for E. coli cells when grown in 22 different conditions so that respective data conversions can be done correctly. First, we determine growth-rate dependent cell volumes. Second, we show that in a 1 ml E. coli sample at an optical density (600 nm) of 1 the total cell volume is around 3.6 µl for all conditions tested. Third, we demonstrate that the cell number in a sample can be determined on the basis of the sample's optical density and the cells' growth rate. The data presented will allow for conversion of E. coli measurement data normalized to optical density into volumetric cellular concentrations and copy numbers per cell--two important parameters for systems biology model development.

/pdf/condition-dependent-cell-volume-and-concentration-of-zdk18cmxvk.pdf

Condition-dependent cell volume and concentration of Escherichia coli to facilitate data conversion for systems biology modeling.

We applied transmission electron microscopy and densitometric image analysis to measure the cell volume (V) and dry weight (DW) of single bacterial cells. The system was applied to measure the DW of Escherichia coli DSM 613 at different growth phases and of natural bacterial assemblages of two lakes, Piburger See and Gossenkollesee. We found a functional allometric relationship between DW (in femtograms) and V (in cubic micrometers) of bacteria (DW = 435.V0.86); i.e., smaller bacteria had a higher ratio of DW to V than larger cells. The measured DW of E. coli cells ranged from 83 to 1,172 fg, and V ranged from 0.1 to 3.5 micron 3 (n = 678). Bacterial cells from Piburger See and Gossenkollesee (n = 465) had DWs from 3 fg (V = 0.003 micron 3) to 1,177 fg (V = 3.5 microns3). Between 40 and 50% of the cells had a DW of less than 20 fg. By assuming that carbon comprises 50% of the DW, the ratio of carbon content to V of individual cells varied from 466 fg of C micron-3 for Vs of 0.001 to 0.01 micron3 to 397 fg of C micron3 (0.01 to 0.1 micron3) and 288 fg of C micron3 (0.1 to 1 micron 3). Exponentially growing and stationary cells of E. coli DSM 613 showed conversion factors of 254 fg of C micron-3 (0.1 to 1 micron3) and 211 fg of C micron-3 (1 to 4 micron3), respectively. Our data suggest that bacterial biomass in aquatic environments is higher and more variable than previously assumed from volume-based measurements.

M. Loferer-Krößbacher

Papers

Determination of Bacterial Cell Dry Mass by Transmission Electron Microscopy and Densitometric Image Analysis