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2008 Annual Science Report

Marine Biological Laboratory Reporting  |  JUL 2007 – JUN 2008

Executive Summary

Earth’s biological history is nominally 3.5 billion years old and fundamentally microbial in character. Our contemporary biosphere contains between 1030 and 1031 microbial genomes, which eclipses the total number of plant and animal cells by at least 2-3 orders of magnitude. Single-cell organisms occupy every imaginable niche ranging from the deep subsurface to the microbiomes of multi-cellular organisms. From the time of their origins, microscopic factories — initially anaerobic and later aerobic — have served as essential catalysts for all of the chemical reactions within biogeochemical cycles that shape planetary change and habitability. Microbial carbon re-mineralization, with and without oxygen, Given the massive number of microbes with seemingly unlimited maintains the carbon cycle. Microbes control global utilization of nitrogen through nitrogen fixation, nitrification, and nitrate reduction, and drive the bulk of sulfur, iron and manganese biogeochemical cycles. They regulate the composition of the atmosphere, influence climates, recycle nutrients, and decompose pollutants. Without microbes, multi-cellular life on earth would not have evolved and biology as we know it would not be sustainable. If life exists on other solar system objects, it will likely be microbial in form.
Recognizing the importance of microbes in the evolution of early life and maintaining habitability, the MBL Astrobiology team has invested in molecular studies that outline patterns of microbial evolution and underlying molecular mechanisms, such as mutational processes and horizontal gene transfer. We investigate the diversity and evolution of microbial communities in extreme environments of the deep ocean, the sub-seafloor and heavy metal-laden, acidic environments that serve as analogues of mars. These investigations have contributed to a new understanding of a long-overlooked aspect of microbial community structures that we refer to as the “rare biosphere. We also explore the genomic consequences of microbial endosymbionts that infect metazoans. These interactions influence both the genomic content of the endosymbionts and shape the population structure of the hosts.
Based upon differences in morphology, biochemical characteristics and metabolic activities, microbiologists traditionally recognized only 5000 different kinds of single cell organisms. Thirty years ago, the introduction of RNA and DNA sequencing technology led to Woese’s discovery of the Archaea. Pace’s introduction of molecular techniques for interrogating microbial communities showed that microbial diversity was one or two orders of magnitude greater than what microbiologists had demonstrated in the laboratory using cultivation technology. Over the past two years, funding from the NAI supported massively parallel DNA sequencing activities that permitted unprecedented sampling efforts of molecular pools that serve as proxies for microbial populations in the Rio Tinto, the deep sub-seafloor and the dark ocean. This work revealed the existence of a rare biosphere where low abundance microbial populations account for new levels of microbial diversity, many of which represent never-before-seen microbial populations. For example, earlier experiments suggested there were no more than 3000 different kinds of microbes in a liter of sea water. Our new massively parallel studies show this may be the case for Archaea but the diversity of Bacterial populations from diffuse flows of the crustal aquifer in the deep ocean exceeds

38,000 different kinds of microbes in a liter of sea water and in a gram of soil microbial richness exceeds 100,000 different kinds of organisms. From these observations we infer that a small number of populations dominate all environments, but thousands of low-abundance organisms account for most of the novel diversity.

In traditional molecular studies, dominant populations have masked the detection of the vast majority of low-abundance OTUs that make up the long tail of taxon-rank distribution curves, their overwhelming genetic diversity, and their individual distribution patterns. The large number of highly diverse, low-abundance OTUs constitutes the rare biosphere. The sum of all different kinds of organisms in the rare biosphere represents a significant fraction of complete microbial communities. The rare biosphere has temporal and spatial dimensions that impact our perceptions of microbial ecology. Some members of the rare biosphere might always represent low-abundance populations irrespective of their location. Others might normally persist in very low numbers but have the capacity to become more abundant in response to environmental change. Finally, some members of the rare biosphere might disperse over long distances from yet to be discovered sites where they are endemic and represent large fractions of a local community. The large diversity of low-abundance taxa relative to entries in the molecular databases reflects the sparse distribution in nature of microbial populations that constitute the rare biosphere. For distinct environments new dominant populations emerge from the rare biosphere. Differences in major populations under dissimilar biogeochemical regimes are hardly unexpected, but the idea that under-represented populations define such enormous diversity with potential to take over a new ecological niche has profound implications.

The concept of a “rare biosphere” forces us to rethink the potential feedback mechanisms between shifts in extremely complex microbial populations and global change, as well as how microbial communities and the genomes of their constituents change over evolutionary time scales. The absence of information about the global distribution of members of the rare biosphere makes it impossible to ascertain if they represent specific biogeographical distributions of bacterial taxa, functional selection by particular environments, or cosmopolitan distribution of all microbial taxa — the Bass Becking idea that all kinds of microbes are everywhere, but the environment selects for the more rapid growth of particular populations. In contrast, it is possible to examine the distribution for abundant tags (corresponding to the most abundant microbes). Figure 3 reveals that some taxa e.g. Pseudomonas, Loktanella, Pseudoaltermonas and SAR 11 are broadly distributed in terrestrial, marine and even habitats within metazo (microbiomes). Other populations display very restricted habitat ranges — e.g. microbes in the Cariaco Basin, symbionts of Sponges and sequences isolated from the Deep subsurface. These microbes with restricted distribution ranges contradict the “everything is everywhere” hypothesis.

More complicated explanations to explain the rare biosphere posit that diversity in microbial populations is comparable to high heterozygosity in animal and plant species. Genetic variability within interbreeding metazoan and plant populations as well as genotypic diversity within microbial communities that exchange genes horizontally could provide the genetic plasticity necessary to overcome exposure to deleterious chemicals, pathogenic agents, the occurrence of unfavorable mutations or changes in environmental conditions i.e. altered temperature extremes, exposure to light, radiation etc. Microorganisms in the long tail of rank-abundance curves might be products of historical ecological change with the potential to become dominant in response to shifts in environmental conditions, e.g. when local or global change favors their growth. The transformation of low-abundance microorganisms into dominant lineages will generally introduce new functional properties that can change the character of the entire ecosystem. These hypotheses elicit many questions including: Are members of the rare biosphere analogous to seed banks that ensure survival after drastic community shifts such as those predicted from global warming? Do the genomes of rare community members contribute to the survival of other phylotypes by contributing new genes and functions through lateral gene transfer events? Is the rare biosphere of archaea and viruses comparable to that of the bacteria? Are some members of the rare biosphere always present at low numbers irrespective of where they occur?

There is no shortage of mechanistic models for sustaining the rare biosphere. Low-abundance populations could be a consequence of slow growing or dormant microbial populations. Rare microbes might detect the presence of like-taxa by quorum-sensing mechanisms that are orders of magnitude more sensitive than those of the more abundant organisms. Frequency-dependent mechanisms predict a survival advantage for rare species, which are less prone to predation and direct competition with dominant community members. However, one of these models account for the extreme phylogenetic diversity represented by the rare biosphere, which suggests its members have persisted over geological time scales. To explain this long-term survival, one might hypothesize that these organisms are keystone species or serve an essential role in maintaining habitability. Finally, the extraordinary length of the long tail is consistent with a model where large numbers of very rare and highly divergent taxa stably coexist because they do not compete for niche space. If there is no competition between rare taxa for niche occupation, the number of different kinds of taxa may be limited only by the total amount of energy available in the ecosystem. An analogy to this model would be the ability of retailers to offer an unlimited number of books on the Internet because there is no competition for limited shelf space.
Microorganisms account for more than 50% of the biomass on the Earth and continue to be the primary engines of planetary cycles of carbon, nitrogen and other elements that regulate the atmospheric composition, soil fertility, the ocean and the global climate. Only human activity rivals the contribution of microbes to climate and environmental change. Our society has doubled the input of reactive nitrogen into the biosphere, directly affecting microbial nutrition, physiology and community composition. Climate warming in the Arctic stimulates soil respiration, adding CO2 to the atmosphere and creating a powerful positive feedback in the climate system, mediated by microbes. Increasing CO2 in the atmosphere is making the oceans warmer and more acidic. We need new ways of thinking to grapple with problems that unfold over decades and centuries; to understand how the smallest of organisms, microbes, can cause impacts on a planetary scale; and to deconstruct the unintended consequences of today’s technology. How will these large changes affect ocean microbes, the largest reservoir of biodiversity on the planet? What will be the impact on microbial contribution to atmospheric gases? Do microbes have the capacity to respond to environmental change and retain the capacity to sustain Earth’s habitability? What mechanisms are key to microbial adaptability to environmental change?
These are but a few of the urgent questions that we must explore in the context of knowing our future and understanding how shifting microbial populations have affected the evolution of habitability on Earth and on other planets. Whether biological systems similar to those on Earth ever occurred or continue to function on other planets or large satellites is unresolved. Given the imprint of life on Earth’s geological record, the presence of comparable biological activity would have a profound effect on the landscapes and atmospheres of other solar system bodies.

The MBL Astrobiology team’s mission-related activities include participate in the OMEGA Imaging spectrometer experiment (Mustard), the HRSC imaging experiment (Head-Co-I), the CRISM imaging spectrometer experiment (Mustard, Co-I) and in the advancement of planetary protection technology (Sogin). Using results from the microbial and physical studies of the Rio Tinto, Mustard and Head achieved a better understanding of Fe sulfates that have been identified in the CRISM data from Mars. As part of the project Preliminary Studies Towards a Microbial Genetic Inventory of Spacecraft rRNA V6-tag sequences, Sogin and collaborators at Berkeley (Anderson) and JPL (Vanket) have developed new methods for evaluating microbial contaminants on out-bound space craft. This project has already identified examples of very significant contamination from humans including the presence of large streptococcal and pseudomonad populations in clean-room environments that would have been missed by NASA’s conventional contamination detection technology.

The EPO efforts of the MBL team have become closely linked to the Astrobiology Biogeocatalysis Research Center and NASA Ames Research Center. We focused on microbes as models for illustrating basic biological concepts while hosting a day of sessions for the MT State Teachers Association and explored extreme environments through a field trip and field guide to Yellowstone NP. We developed a new course “Astrobiology: Extreme Environments” for the MSU M.S. in Science Education program piloting the AstroMicroBiology Group activities (Kelly, Bebout and Bahr) Our next step, with the IPTAI team, is distribution through the National Association of Biology Teachers conference. MBL scientists used NAI videoconferencing to meet with teachers at MSU and at DePaul University. Finally, we have been involved in our own community, especially through the Falmouth Kids Global Climate Change Institute Program.