Source: UNIV OF MASSACHUSETTS submitted to
AMAZON RAINFOREST MICROBIAL OBSERVATORY: FUNCTIONAL DIVERSITY, TAXONOMIC DIVERSITY, AND RESPONSE TO ECOSYSTEM CONVERSION
 
PROJECT DIRECTOR: Nusslein, K. R. Tiedje, J. M. Bohannan, B. J. Rodrigues, J. L.
 
PERFORMING ORGANIZATION
MICROBIOLOGY
UNIV OF MASSACHUSETTS
AMHERST,MA 01003
 
NON TECHNICAL SUMMARY: Understanding the causes and consequences of biological diversity is a central goal of biology. Studies of the diversity of plants and animals have shown that biodiversity is heterogeneously distributed across the Earth, with a few regions that contain the majority of plant and animal diversity. One of the best studied is the rainforest of Amazonia, Brazil. This region is under great threat; conversion to agriculture has resulted in the loss of over 17% of the original rainforest. At this rate, the Amazon rainforest could cease to exist by the end of the century. Despite its great plant and animal diversity, and its long history of diversity studies, the Amazon rainforest is among the least understood ecosystems regarding bacterial diversity. There is reason to believe that microbial diversity could be very high in this region. First, the high diversity of macroorganism species in the region reflects the great environmental variation present, variation that could also result in very high microbial diversity. Second, the existence of such high macroorganism diversity could provide a wide variety of substrates for microbial metabolism. However, there currently exist only three very limited studies of bacterial diversity in the Amazon rainforest, and these studies present very conflicting views regarding the diversity of bacterial life. In addition, nothing is known how agriculutural land use change influences soil bacterial diversity patterns in this region. We propose to establish a Microbial Observatory (MO) in the Amazon rainforest. The proposed Observatory will have three overarching goals: to search for biological novelty, to describe the bacterial communities of Amazon rainforest soil, and to determine the effect of agricultural conversion on these communities. We will use intensive and extensive culture-independent methods, combined with novel culture-dependent methods, to achieve these goals. This proposal describes a four-year, multi-PI effort to investigate the bacterial diversity of the native Amazonian rainforest, and how agriculturally driven ecosystem conversion can alter this diversity. The research plan will be completed through a strong interdisciplinary and collaborative effort between the University of Massachusetts (PI Nnsslein), Michigan State University (Co-PI Tiedje), the University of Texas at Arlington (Co-PI Rodrigues), and the University of Oregon (Co-PI Bohannan). This proposal offers the following advantages: It determines rainforest soil microbial diversity. It is focused on the largest planet ecosystem. It combines different taxonomic and functional levels of diversity analysis. It utilizes three measures of diversity. It considers spatial diversity analysis. Discovery of novelty through isolation of Acidobacteria. Consideration of two microbial groups with different ecophysiological strategies. Archive for a large soil databank available to other researchers.
 
OBJECTIVES: An increasing demand for grain, fibers, and biofuel has accelerated the relentless conversion of the Amazon ecosystem to agriculture, creating a new frontier of deforestation of 1 million sq. km. The consequences of this shift are expected to be significant to global emissions of greenhouse gases, global warming, soil degradation, and water resources. Macro-biological studies of the diversity of plant and animals have revealed the rainforest as one of the biodiversity hotspots. However, the Amazon rainforest, credited as the largest biological reservoir of animal and plant species on Earth, is among the least understood ecosystems regarding bacterial diversity. The forest soil microbial diversity is poorly characterized and the only three studies currently present conflicting views about its microbiological diversity. Understanding the causes, patterns, and consequences of soil microbiological diversity and its importance to the rainforest soil ecosystem function is a central goal of this Microbial Observatory. We propose to establish baseline diversity at broad coverage in the Amazon rainforest, and determine how microbial diversity changes in response to land use by ecosystem conversion from rainforest to agriculture. Our conceptual model for this research is guided by three questions: 1. Do magnitude and spatial scaling of microbial diversity mirror that of tropical plant and animal diversity 2. Are spatial patterns in soil microbial diversity less pronounced at higher levels of taxonomic resolution[unclear, remove altogether] 3. Is the bacterial diversity in Amazon Forest reduced by agricultural development The range of Expected Outputs and Impacts of the proposed research will be consolidated through enhancing international collaboration with a team of Brazilian biogeochemists and microbiologists. It will allow postdoctoral research associates and undergraduate students to interact with their Brazilian peers to exchange scientific information, giving them a chance to think globally and to learn from different perspectives, and will provide educational opportunities through training on state of the art genome sequencing techniques, metagenomics annotation, spatial patterns of functional genes, isolation, and taxonomic classification. By disseminating our results widely, we will improve understanding of microbial diversity at different levels of resolution: spatial distribution patterns, and gene patterns linked to habitat. We will not only establish previously unavailable base line data on tropical soil diversity, but investigate also the impact ecosystem conversion has on that diversity. This will allow us to better estimate consequences of common agricultural conversions. In addition, we will define the level of resolution at which soil bacterial diversity is established.
 
APPROACH: Soil is often avoided in Microbial Ecology studies in favor of environmental extremes to encounter a more manageable level of bacterial diversity. In this MO we directly target soil microbial diversity in the largest plant ecosystem in the world. We will assess the genomic variability of members of the genus Burkholderia as one measure of diversity, and follow the shift in Burkholderia diversity from native rainforest via the impact of deforestation to agricultural monoculture. Measurements of diversity of N2 fixation characteristics of Burkholderia strains corroborate this study at a functional level. This work will contribute better estimates soil microbial diversity in Amazonia, one of largest biological reservoir of world, and how and at what level of resolution that diversity follows a pattern. Our strategy to discover biological novelty and how it is influenced by agriculturally driven land use change is as follows. We will determine tropical bacterial diversity at several levels of resolution using culture dependent vs. culture independent approaches, and investigate how diversity is influenced by landscape changes. Our initial attempt to answer "Who is there" will be discovery driven to establish a baseline of bacterial diversity in the Amazon. Dominant and rare species composition will be described at high coverage using a variant of the 454 sequencing technology, called Ultra-Deep Sequencing. Species composition will be paralleled by a characterization of the diversity of known functional genes based on the extensive gene microarray termed GeoChip and round up the core datasets for diversity. To address the question whether agricultural development alters this diversity we will engage a hypothesis driven research approach in which we employ both culture independent as well as culture dependent techniques across a chronosequence of four land uses. The above listed DNA based core diversity analyses will be applied to all treatments. To deepen our insight into diversity shifts we will then focus on the common soil bacterial genera Burkholderia and Acidobacteria as a proxy of influences on diversity. In an extension of the massively parallel 454 sequencing technique we termed Multi Locus Community Profiling we will characterize and compare the functional and taxonomic diversity of defined target genes of both genera within the soil community. For select soil samples traditional clone library analysis of the gene for nitrogen fixation, nifH, and recA will confirm MLCP. Burkholderia diversity can then be efficiently speciated using a Burkholderia Phyloarray. The array will help with grouping the isolates. Culture independent analyses will be paralleled by strategic attempts to isolate a large variety of Burkholderia and Acidobacteria. Hypothesizing that different ecological strategies for survival are imprinted in the isolates genomes, we will apply Multi Locus Sequencing Typing to investigate genomic patterns of isolates relative to soil treatments.
 
CRIS NUMBER: 0216773 SUBFILE: CRIS
PROJECT NUMBER: MAS0200804556 SPONSOR AGENCY: NIFA
PROJECT TYPE: NRI COMPETITIVE GRANT PROJECT STATUS: NEW MULTI-STATE PROJECT NUMBER: (N/A)
START DATE: Jan 1, 2009 TERMINATION DATE: Dec 31, 2012

GRANT PROGRAM: BIOLOGY OF PLANT-MICROBE ASSOC.
GRANT PROGRAM AREA: Plant Systems

CLASSIFICATION
Knowledge Area (KA)Subject (S)Science (F)Objective (G)Percent
131019911006.110%
131064011006.110%
131401011006.130%
136019911006.310%
136064011006.310%
136401011006.330%

CLASSIFICATION HEADINGS
KA131 - Alternative Uses of Land
KA136 - Conservation of Biological Diversity
S0199 - Soil and land, general
S4010 - Bacteria
S0640 - Tropical forests
F1100 - Bacteriology
G6.1 - Ensure Clean Water and Air
G6.3 - Protect and Manage Forests and Rangelands


RESEARCH EFFORT CATEGORIES
BASIC 70%
APPLIED 10%
DEVELOPMENTAL 20%

KEYWORDS: amazon rainforest~soil microbiology~soil microbial diversity~land use change~microbial observatory~454 sequencing~biological novelty~spatial diversity~acidobacteria~burkholderia~multi locus community profiling~soybean

PROGRESS: TO
(N/A)

IMPACT: TO (N/A)

PUBLICATION INFORMATION: TO


PROJECT CONTACT INFORMATION
NAME: Cromack, P.
PHONE: 413-545-5913
FAX: 413-545-1977