Biofilmsubsidiesfigs06252013.001

Charles Pepe-Ranney

and 1 more

INTRODUCTION Biofilms are diverse and complex microbial consortia, and, the biofilm lifestyle is the rule rather than the exception for microbes in many environments. Large and small-scale biofilm architectural features play an important role in their ecology and influence their role in biogeochemical cycles . Fluid mechanics impact biofilm structure and assembly , but it is less clear how other abiotic factors such as resource availability affect biofilm assembly. Aquatic biofilms initiate with seed propagules from the planktonic community . Thus, resource amendments that influence planktonic communities may also influence the recruitment of microbial populations during biofilm community assembly. In a crude sense, biofilm and planktonic microbial communities divide into two key groups: oxygenic phototrophs including eukaryotes and cyanobacteria (hereafter “photoautotrophs”), and heterotrophic bacteria and archaea. This dichotomy, admittedly an abstraction (e.g. non-phototrophs can also be autotrophs), can be a powerful paradigm for understanding community shifts across ecosystems of varying trophic state . Heterotrophs meet some to all of their organic carbon (C) requirements from photoautotroph produced C while simultaneously competing with photoautotrophs for limiting nutrients such as phosphorous (P) . The presence of external C inputs, such as terrigenous C leaching from the watershed or C exudates derived from macrophytes , can alleviate heterotroph reliance on photoautotroph derived C and shift the heterotroph-photoautotroph relationship from commensal and competitive to strictly competitive . Therefore, increased C supply should increase the resource space available to heterotrophs and increase competition for mineral nutrients decreasing nutrients available for photoautotrophs (assuming that heterotrophs are superior competitors for limiting nutrients as has been observed ). These dynamics should result in the increase in heterotroph biomass relative to the photoautotroph biomass along a gradient of increasing labile C inputs. We refer to this differential allocation of limiting resources among components of the microbial community as niche partitioning. While these gross level dynamics have been discussed conceptually and to some extent demonstrated empirically , the effects of biomass dynamics on photoautotroph and heterotroph membership and structure has not been directly evaluated in plankton or biofilms. In addition, how changes in planktonic communities propagate to biofilms during community assembly is not well understood. We designed this study to test if C subsidies shift the biomass balance between autotrophs and heterotrophs within the biofilm or its seed pool (i.e. the plankton), and, to measure how changes in biomass pool size alter composition of the plankton and biofilm communities. Specifically, we amended marine mesocosms with varying levels of labile C input and evaluated differences in photoautotroph and heterotrophic bacterial biomass in plankton and biofilm samples along the C gradient. In each treatment we characterized plankton and biofilm community composition by PCR amplifying and DNA sequencing 16S rRNA genes and plastid 23S rRNA genes.
Ordination heavy day facet

Charles Pepe-Ranney

and 3 more

ABSTRACT Biological soil crusts (BSC) are key components of ecosystem productivity in arid lands and they cover a substantial fraction of the terrestrial surface. In particular, BSC N₂-fixation contributes significantly to the nitrogen (N) budget of arid land ecosystems. In mature crusts, N₂-fixation is largely attributed to heterocystous cyanobacteria, however, early successional crusts possess few N₂-fixing cyanobacteria and this suggests that microorganisms other than cyanobacteria mediate N₂-fixation during the critical early stages of BSC development. DNA stable isotope probing (DNA-SIP) with ¹⁵N₂ revealed that _Clostridiaceae_ and _Proteobacteria_ are the most common microorganisms that assimilate ¹⁵N₂ in early successional crusts. The _Clostridiaceae_ identified are divergent from previously characterized isolates, though N₂-fixation has previously been observed in this family. The Proteobacteria identified share >98.5 %SSU rRNA gene sequence identity with isolates from genera known to possess diazotrophs (e.g. _Pseudomonas_, _Klebsiella_, _Shigella_, and _Ideonella_). The low abundance of these heterotrophic diazotrophs in BSC may explain why they have not been characterized previously. Diazotrophs play a critical role in BSC formation and characterization of these organisms represents a crucial step towards understanding how anthropogenic change will affect the formation and ecological function of BSC in arid ecosystems. KEYWORDS: microbial ecology / stable isotope probing / nitrogen fixation / biological soil crusts