For two centuries, biologists have documented a gradient of animal and plant biodiversity from the tropics to the poles but have been unable to agree whether it is controlled primarily by ...productivity, temperature, or historical factors. Recent reports that find latitudinal diversity gradients to be reduced or absent in some unicellular organisms and attribute this to their high abundance and dispersal capabilities would suggest that bacteria, the smallest and most abundant organisms, should exhibit no latitudinal pattern of diversity. We used amplified ribosomal intergenic spacer analysis (ARISA) whole-assemblage genetic fingerprinting to quantify species richness in 103 near-surface samples of marine bacterial plankton, taken from tropical to polar in both hemispheres. We found a significant latitudinal gradient in richness. The data can help to evaluate hypotheses about the cause of the gradient. The correlations of richness with latitude and temperature were similarly strong, whereas correlations with parameters relating to productivity (chlorophyll, annual primary productivity, bacterial abundance) and other variables (salinity and distance to shore) were much weaker. Despite the high abundance and potentially high dispersal of bacteria, they exhibit geographic patterns of species diversity that are similar to those seen in other organisms. The latitudinal gradient in marine bacteria supports the hypothesis that the kinetics of metabolism, setting the pace for life, has strong influence on diversity.
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BFBNIB, NMLJ, NUK, PNG, SAZU, UL, UM, UPUK
Predicting the variation of biodiversity across the surface of the Earth is a fundamental issue in ecology, and in this article we focus on one of the most widely studied spatial biodiversity ...patterns: the species-area relationship (SAR). The SAR is a central tool in conservation, being used to predict species loss following global climate change, and is striking in its universality throughout different geographical regions and across the tree of life. In this article we draw upon the methods of quantum field theory and the foundation of neutral community ecology to derive the first spatially explicit neutral prediction for the SAR. We find that the SAR has three phases, with a power law increase at intermediate scales, consistent with decades of documented empirical patterns. Our model also provides a building block for incorporating non-neutral biological variation, with the potential to bridge the gap between neutral and niche-based approaches to community assembly. Ecology Letters (2010) 13: 87-95
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Microorganisms have shaped our planet and its inhabitants for over 3.5 billion years. Humankind has had a profound influence on the biosphere, manifested as global climate and land use changes, and ...extensive urbanization in response to a growing population. The challenges we face to supply food, energy, and clean water while maintaining and improving the health of our population and ecosystems are significant. Given the extensive influence of microorganisms across our biosphere, we propose that a coordinated, cross-disciplinary effort is required to understand, predict, and harness microbiome function. From the parallelization of gene function testing to precision manipulation of genes, communities, and model ecosystems and development of novel analytical and simulation approaches, we outline strategies to move microbiome research into an era of causality. These efforts will improve prediction of ecosystem response and enable the development of new, responsible, microbiome-based solutions to significant challenges of our time.
Power-law frequency distributions characterize a wide array of natural phenomena. In ecology, biology, and many physical and social sciences, the exponents of these power laws are estimated to draw ...inference about the processes underlying the phenomenon, to test theoretical models, and to scale up from local observations to global patterns. Therefore, it is essential that these exponents be estimated accurately. Unfortunately, the binning-based methods traditionally used in ecology and other disciplines perform quite poorly. Here we discuss more sophisticated methods for fitting these exponents based on cumulative distribution functions and maximum likelihood estimation. We illustrate their superior performance at estimating known exponents and provide details on how and when ecologists should use them. Our results confirm that maximum likelihood estimation outperforms other methods in both accuracy and precision. Because of the use of biased statistical methods for estimating the exponent, the conclusions of several recently published papers should be revisited.
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Urban green space provides health benefits for city dwellers, and new evidence suggests that microorganisms associated with soil and vegetation could play a role. While airborne microorganisms are ...ubiquitous in urban areas, the influence of nearby vegetation on airborne microbial communities remains poorly understood. We examined airborne microbial communities in parks and parking lots in Eugene, Oregon, using high-throughput sequencing of the bacterial 16S rRNA gene on the Illumina MiSeq platform to identify bacterial taxa, and GIS to measure vegetation cover in buffer zones of different diameters. Our goal was to explore variation among highly vegetated (parks) versus non-vegetated (parking lots) urban environments. A secondary objective was to evaluate passive versus active collection methods for outdoor airborne microbial sampling. Airborne bacterial communities from five parks were different from those of five parking lots (p=0.023), although alpha diversity was similar. Direct gradient analysis showed that the proportion of vegetated area within a 50m radius of the sampling station explained 15% of the variation in bacterial community composition. A number of key taxa, including several Acidobacteriaceae were substantially more abundant in parks, while parking lots had higher relative abundance of Acetobacteraceae. Parks had greater beta diversity than parking lots, i.e. individual parks were characterized by unique bacterial signatures, whereas parking lot communities tended to be similar to each other. Although parks and parking lots were selected to form pairs of nearby sites, spatial proximity did not appear to affect compositional similarity. Our results also showed that passive and active collection methods gave comparable results, indicating the “settling dish” method is effective for outdoor airborne sampling. This work sets a foundation for understanding how urban vegetation may impact microbial communities, with potential implications for designing neighborhoods and open space systems that foster better human health.
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•We compared airborne bacterial samples from parks and parking lots with 16S sequencing.•Bacterial communities from parks and parking lots were compositionally distinct.•Proportion of vegetated area within 50m explained 15% of the variation among samples.•Parking lots had similar bacterial signatures, but parks tended to be unique.•Passive and active collection methods gave comparable results.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
The role of ecological theory in microbial ecology Prosser, James I; Bohannan, Brendan J. M; Curtis, Tom P ...
Nature reviews. Microbiology,
200705, 2007-May, 2007-5-00, 20070501, Volume:
5, Issue:
5
Journal Article
Peer reviewed
Open access
Microbial ecology is currently undergoing a revolution, with repercussions spreading throughout microbiology, ecology and ecosystem science. The rapid accumulation of molecular data is uncovering ...vast diversity, abundant uncultivated microbial groups and novel microbial functions. This accumulation of data requires the application of theory to provide organization, structure, mechanistic insight and, ultimately, predictive power that is of practical value, but the application of theory in microbial ecology is currently very limited. Here we argue that the full potential of the ongoing revolution will not be realized if research is not directed and driven by theory, and that the generality of established ecological theory must be tested using microbial systems.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Most people on the planet own mobile phones, and these devices are increasingly being utilized to gather data relevant to our personal health, behavior, and environment. During an educational ...workshop, we investigated the utility of mobile phones to gather data about the personal microbiome - the collection of microorganisms associated with the personal effects of an individual. We characterized microbial communities on smartphone touchscreens to determine whether there was significant overlap with the skin microbiome sampled directly from their owners. We found that about 22% of the bacterial taxa on participants' fingers were also present on their own phones, as compared to 17% they shared on average with other people's phones. When considered as a group, bacterial communities on men's phones were significantly different from those on their fingers, while women's were not. Yet when considered on an individual level, men and women both shared significantly more of their bacterial communities with their own phones than with anyone else's. In fact, 82% of the OTUs were shared between a person's index and phone when considering the dominant taxa (OTUs with more than 0.1% of the sequences in an individual's dataset). Our results suggest that mobile phones hold untapped potential as personal microbiome sensors.
Buildings represent habitats for microorganisms that can have direct or indirect effects on the quality of our living spaces, health, and well-being. Over the last ten years, new research has ...employed sophisticated tools, including DNA sequencing-based approaches, to study microbes found in buildings and the overall built environment. These investigations have catalyzed new insights into and questions about the microbes that surround us in our daily lives. The emergence of the “microbiology of the built environment” field has required bridging disciplines, including microbiology, ecology, building science, architecture, and engineering. Early insights have included a fuller characterization of sources of microbes within buildings, important processes that structure the distributions and abundances of microbes, and a greater appreciation of the role that occupants can have on indoor microbiology. This ongoing work has also demonstrated that traditional culture- and microscopy-based approaches for studying microbiology vastly underestimate the types and quantity of microbes present in environmental samples. We offer ten questions that highlight important lessons learned regarding the microbiology of buildings and suggest future areas of investigation.
•Research interest in the microbiology of the built environment has increased in recent years.•The built environment houses a great diversity of microorganisms.•Emerging research has elucidated the sources and spatial, temporal, and taxonomic distribution of microorganisms in buildings.•Building operation, ventilation, and occupancy drives the building microbiology.•The role of built environment microbiology on occupant health is an active area of research.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Dispersal of microbes between humans and the built environment can occur through direct contact with surfaces or through airborne release; the latter mechanism remains poorly understood. Humans emit ...upwards of 10(6) biological particles per hour, and have long been known to transmit pathogens to other individuals and to indoor surfaces. However it has not previously been demonstrated that humans emit a detectible microbial cloud into surrounding indoor air, nor whether such clouds are sufficiently differentiated to allow the identification of individual occupants. We used high-throughput sequencing of 16S rRNA genes to characterize the airborne bacterial contribution of a single person sitting in a sanitized custom experimental climate chamber. We compared that to air sampled in an adjacent, identical, unoccupied chamber, as well as to supply and exhaust air sources. Additionally, we assessed microbial communities in settled particles surrounding each occupant, to investigate the potential long-term fate of airborne microbial emissions. Most occupants could be clearly detected by their airborne bacterial emissions, as well as their contribution to settled particles, within 1.5-4 h. Bacterial clouds from the occupants were statistically distinct, allowing the identification of some individual occupants. Our results confirm that an occupied space is microbially distinct from an unoccupied one, and demonstrate for the first time that individuals release their own personalized microbial cloud.
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