Both bacteria and fungi play critical roles in decomposition processes in many natural environments, yet only rarely have they been studied as an integrated microbial community. Here we describe the bacterial and fungal assemblages associated with two decomposition stages of Spartina alterniflora detritus in a productive southeastern U.S. salt marsh. 16S rRNA genes and 18S-to-28S internal transcribed spacer (ITS) regions were used to target the bacterial and ascomycete fungal communities, respectively, based on DNA sequence analysis of isolates and environmental clones and by using community fingerprinting based on terminal restriction fragment length polymorphism (T-RFLP) analysis. Seven major bacterial taxa (six affiliated with the ␣-Proteobacteria and one with the Cytophagales) and four major fungal taxa were identified over five sample dates spanning 13 months. Fungal terminal restriction fragments (T-RFs) were informative at the species level; however, bacterial T-RFs frequently comprised a number of related genera. Amplicon abundances indicated that the salt marsh saprophyte communities have little-to-moderate variability spatially or with decomposition stage, but considerable variability temporally. However, the temporal variability could not be readily explained by either successional shifts or simple relationships with environmental factors. Significant correlations in abundance (both positive and negative) were found among dominant fungal and bacterial taxa that possibly indicate ecological interactions between decomposer organisms. Most associations involved one of four microbial taxa: two groups of bacteria affiliated with the ␣-Proteobacteria and two ascomycete fungi (Phaeosphaeria spartinicola and environmental isolate "4clt").Southeastern U.S. coastal salt marshes are among the most productive ecosystems known (24, 31) and provide a model environment for investigating detritus-based ecosystems and their decomposer communities. In these systems, both fungi and bacteria are recognized as key components of the decomposer community (1, 26), providing primary links in the remineralization and transformation of decaying vascular plant material.In the few studies that have considered the activity of salt marsh bacterial and fungal saprophytes simultaneously, interactions between fungi and bacteria have been hypothesized to be based on temporal resource partitioning (29). According to this view, fungal colonization of senescing salt marsh cord grass (Spartina alterniflora) mediates the initial transformation of organic matter through extracellular enzyme activity and physical disruption (24, 26). In the fungus-dominated stage, Spartina undergoes loss of up to 60% of the original organic mass (26). As decomposition proceeds, the blades gradually collapse onto the marsh sediment and are reduced to smaller pieces with larger surface areas. Bacterial standing crop gradually increases, and bacteria assume a more prominent position in the latter stages of the decomposition process (1,29).This view of temporally...
Hands play a critical role in the transmission of microbiota on one’s own body, between individuals, and on environmental surfaces. Effectively measuring the composition of the hand microbiome is important to hand hygiene science, which has implications for human health. Hand hygiene products are evaluated using standard culture-based methods, but standard test methods for culture-independent microbiome characterization are lacking. We sampled the hands of 50 participants using swab-based and glove-based methods prior to and following four hand hygiene treatments (using a nonantimicrobial hand wash, alcohol-based hand sanitizer [ABHS], a 70% ethanol solution, or tap water). We compared results among culture plate counts, 16S rRNA gene sequencing of DNA extracted directly from hands, and sequencing of DNA extracted from culture plates. Glove-based sampling yielded higher numbers of unique operational taxonomic units (OTUs) but had less diversity in bacterial community composition than swab-based sampling. We detected treatment-induced changes in diversity only by using swab-based samples (P < 0.001); we were unable to detect changes with glove-based samples. Bacterial cell counts significantly decreased with use of the ABHS (P < 0.05) and ethanol control (P < 0.05). Skin hydration at baseline correlated with bacterial abundances, bacterial community composition, pH, and redness across subjects. The importance of the method choice was substantial. These findings are important to ensure improvement of hand hygiene industry methods and for future hand microbiome studies. On the basis of our results and previously published studies, we propose recommendations for best practices in hand microbiome research.
Vibrio fischeri isolates from Euprymna scolopes are dim in culture but bright in the host. We found the luminescence of V. fischeri to be correlated with external osmolarity both in culture and in this symbiosis. Luminescence enhancement by osmolarity was independent of the lux promoter and unaffected by autoinducers or the level of lux expression, but the addition of an aldehyde substrate for luciferase raised the luminescence of cells grown at high and low osmolarities to the same high level. V. fischeri culture media have lower osmolarities than are typical in seawater or in cephalopods, partially accounting for the bacterium's low light output in culture.The light organ symbiosis between the bioluminescent bacterium Vibrio fischeri and the Hawaiian bobtailed squid Euprymna scolopes has been developed as a model for studying mutualistic animal-bacterium interactions (15,21). In establishing this system in our laboratory, we discovered that E. scolopes juveniles infected with V. fischeri in artificial seawater (Instant Ocean; Aquarium Systems, Mentor, Ohio) lost luminescence after 3 days, but remained colonized, if they were kept in diluted seawater (700 to 850 mosM) rather than seawater mixed to marine concentrations (975 to 1,025 mosM). Figure 1 illustrates this phenomenon with the results of one representative experiment. Squid were infected as previously described (16), and their luminescence was measured with a model LS 6500 counter (Beckman Coulter, Fullerton, Calif.). Although marine organisms are sometimes maintained at relatively low osmolarities, our data highlight the fact that this can perturb their natural biology in important ways.These data were intriguing because luminescence contributes to colonization persistence (20), and V. fischeri isolates from E. scolopes are unusual in that they are dim in culture (even dense culture) and bright only in the host (1, 10). Our data show wild-type cells exhibiting a dimness like that seen in culture in fully colonized squid, suggesting that we had mimicked culture conditions by placing the animals in dilute seawater. A simple explanation for our observations of symbiotic luminescence was that the squid, which maintain hyperosmotic tissues, lost the ability to osmoregulate against an unnaturally steep gradient and that the luminescence of the V. fischeri symbionts was dependent on the osmolarity of their surroundings (e.g., the light organ crypts). Consistent with the latter part of this model, in 1950 Farghaly reported a correlation between osmolarity and luminescence in culture for a bacterium that was probably a planktonic V. fischeri isolate (7).We therefore tested the relationship between osmolarity and luminescence in a wild-type E. scolopes isolate, V. fischeri strain ES114 (1). Medium osmolarity was assessed using a freezingpoint depression-automated osmometer (Osmette A; Precision Systems Inc., Natick, Mass.). The optical density at 595 nm (OD 595 ) was determined with a BioPhotometer (Brinkmann Instruments Inc., Westbury, N.Y.) by measuring the cu...
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