College of Natural Resources, UC Berkeley

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February 27, 2004

Stephens Testifies on Sierra Nevada Forest Plan

The Subcommittee on Forests and Forest Health has invited CNR Assistant Professor Scott Stephens to testify at a Feb. 28 field hearing on the Sierra Nevada Forest Plan: Protecting Communities, Water, Wildlife and Forests in the Sierra Nevada in Jackson, Calif. Stephens testimony is below.

The United States Forest Service (USFS) lands in the Sierra Nevada and Southern Cascades are incredible national treasures. These lands provide clean water, recreational opportunities, timber, oxygen, forage, and spiritual values. I believe everyone at this hearing is connected to these lands in multiple ways.

The USFS has been engaged in large-scale land management planning in this region since 1990. The first guidelines developed during this period were the Interim California Spotted Owl Guidelines. They were forecasted to last for only 1-3 years. At the end of this period a full land management plan for all USFS lands in this region was expected to have been finished.

During the last 7 years we have seen the USFS develop 2 more Environmental Impact Statements for this region. The first was developed under the Clinton administration and a record of decision was signed a couple of weeks before the Bush administration took office. Shortly after the new administration came into office a review of this decision was implemented. This resulted in the development of a Draft Supplemental Environmental Impact Statement. Public comments were accepted, and about 1 month ago, the USFS released the Final Supplemental Environmental Impact Statement. It should be noted that the previous USFS plan (Sierra Nevada Framework) really was not given a chance to succeed or fail. Although several USFS Region 5 line officers have stated that it was too cumbersome and included many contradictions, it was not implemented at any significant scale.

The time, effort, and resources devoted to these multiple plans have been very large. There are real fire and ecosystem issues that need to be addressed in this region but we continue to spend enormous amounts of time and energy in the planning phase. This period has also resulted in tremendous debates from environmental groups, timber companies, recreational users, livestock managers, and the public. This debate continues to the present.

Today I will present a discussion of wildland fire issues in the Sierra Nevada and Southern Cascades. This will include a discussion of fire hazards in the forests of this region, landscape fuel treatment designs, issues concerning the urban wildland intermix (UWI), and probably most important of all, the need for a comprehensive strategy to implement a land management plan in this region.

Reduction of Potential Fire Behavior in Mixed Conifer, Ponderosa Pine, and Jeffrey Pine Forests

The ponderosa pine, mixed conifer, and Jeffrey pine forests in this region have been modified over the last century because of fire suppression, livestock grazing, timber harvests, and possibly changes in climate. The results include a general deterioration in forest ecosystem integrity and an increased probability of large, highseverity wildfires. Such conditions are prevalent nationally, especially in forests that once experienced short-interval (< 15 years), low to moderate-severity fire regimes.

Along with increased fire hazards these forests also have multiple ecosystem problems. Fire suppression and selective harvests have increased the abundance of shade tolerant tree species such as white fir and incense-cedar. In many areas past harvests have removed most of the largest trees. Shade intolerant species such as California black oak have declined over the last century. This species has been identified as crucial for many wildlife species in this region. Other shade intolerant species such as ponderosa pine and giant sequoia have declined as well.

The need for restoration is clear. Less clear are the desired future conditions for these diverse forests and what should be done to achieve and maintain them. The recent tree mortality in the forests in southern California remind us that ecosystems are constantly changing and in some cases, the outcome of these changes are not desirable. We must develop the ability to restore and maintain the forests of this region.

Fuels reduction is the central theme in the current USFS management plan. The objective of such treatments should be a reduction of potential fire behavior, not simply the reduction of forest fuels. Fire behavior is a function of fuels, weather, and topography. Fuels are the major fire behavior component that can be directly affected by management. Local climate conditions can also be influenced by treatments resulting in tradeoffs between reducing canopy cover and opening up stands that increases air temperatures and wind speeds, and decreases relative humidity and fuel moisture contents.

Wildland fuels are separated into four groups (ground, surface, ladder, crown) and each has a different potential to influence fire behavior. Ground fuels include the duff and litter on the soil surface and they do not usually contribute to wildfire spread or intensity. Surface fuels include all dead and down woody materials, grasses, other herbaceous plant materials, and short shrubs, and these are often the most hazardous fuels in forests that have been influenced by 100 years of fire suppression. Ladder fuels are small trees or tall shrubs that provide vertical continuity from surface fuels to the crowns of tall tress. Crown fuels are those in the overstory.

Reducing surface fuels will limit the intensity of fires, provide a higher probability of controlling wildfires, and allow more of the forest to survive when it does burn. Thinning treatments can be directed to effectively reduce ladder and crown fuels. However, if logging residues (activity fuels) are left on site, this can result in potential fire behavior that is more extreme or similar to the untreated forest. Fuels treatments in forests that once experienced frequent, low-moderate intensity fire regimes must focus on surface, ladder, and then crown fuels. Surface fuel reduction cannot be an afterthought of fuel treatments in these forests, it must be the central objective. The current USFS plan does not place enough emphasis on surface fuels. Instead it concentrates on ladder and crown fuels and this is a mistake. It is an example of good intentions that simply misses the mark.

An excellent example of this principle occurred at the Blacks Mountain Experimental Forest located in the Southern Cascades, an area covered by the present USFS management plan. A wildfire burned several experimental units 2 years ago that had been designed to investigate the impacts of forest harvesting on several ecosystem elements. Blacks Mountain is primarily a ponderosa pine forest and it is in the surrounded by the Lassen National Forest.

The treatments that were burned by the wildfire included low diversity alone, low diversity followed by prescribed fire, high diversity followed by prescribed fire, and controls. The high diversity treatment consisted of a thinning from below and all large overstory trees were retained. The low diversity treatments consisted of an overstory removal (all large trees harvested) followed by lop and scatter of the activity fuels and then a whole tree harvesting of the sub-merchantable trees. The whole tree harvest removed the majority of the ladder fuels and left no additional activity fuels.

When the wildfire entered the high diversity unit that had also been prescribe burned, it transitioned from a high severity crown fire to a very low intensity surface fire in about 200 feet. The treated forest almost stopped the wildfire in this unit. In the low diversity unit that had been prescribed burned a similar change in fire behavior occurred, from a severe crown fire to a low intensity surface fire in less than 200 feet. When the wildfire moved into the low diversity unit that had not been prescribe burned, the wildfire changed from a serve crown fire to a severe surface fire. The severe surface fire burned the majority of the unit and this killed approximately 60-80 percent of the trees. The wildfire burned in this unit because the activity and natural fuels were sufficient to carry the wildfire. If this treatment had also left the sub- merchantable trees on the ground as activity fuels, I am sure the whole unit would have experienced almost complete mortality. This occurred even though canopy cover, crown bulk density, and ladder fuels were very low in the low diversity units. Trees were widely spaced by the low diversity treatment and no crowns were overlapping. It simply provides more support that the target of almost all fuel treatments in mixed conifer, ponderosa pine, and Jeffrey pine forests must be the surface fuels. I would also add that the control units that were burned by the wildfire were totally destroyed, further reinforcing that effective treatments are needed to reduce fire hazards in these ecosystems.

Removal of moderately sized trees (20- 30 inches in diameter) can produce revenue and wood products for California, but in the majority of cases, it will not significantly reduce potential fire behavior. Removal of trees of this size will only reduce canopy bulk density and this will have a small affect on potential fire behavior in most forest stands. The target of fuels projects must be the surface and ladder fuels.

Since fire hazard reduction has never been the main objective of USFS land management, we have no large-scale research or demonstration projects to support such a management philosophy. There simply are no places to go in California or elsewhere, to get information on the trade-offs (economic, social, ecological) of large-scale management treatments designed to reduce potential fire behavior and improve forest sustainability. The final USFS plan selected for this region will be able to address this key issue if a strong monitoring and adaptive management strategy is included. This portion of the current plan needs significant improvement.

Landscape Treatments Designed to Reduce Fire Behavior

The use of Strategically Placed Area Treatments (SPLAT’s) and Defensive Fuel Profile Zones (DFPZ’s) can be used in a landscape strategy to reduce potential fire behavior.
SPLAT’s are a system of overlapping area fuel treatments designed to minimize the area burned by high intensity head-fires in diverse terrain and may be an effective strategy to reduce landscape fire behavior in large, heterogeneous areas. Human-caused fires commonly occur near transportation corridors (highways, roads, trails), campgrounds, and urban areas, making it possible for fire managers to forecast areas of higher ignition potential. DFPZ’s placed near areas of high human-caused ignitions can be used to decrease the probability of large, high-severity fires, by improving suppression efficiency. Installation and maintenance of these structures (SPLAT’s and DFPZ’s) at appropriate spatial scales should reduce landscape forest fire area and severity.

This area of the current USFS management plan should be substantially expanded to include both stand level and landscape level analysis of proposed fuels treatments. It may be true that the models used in the USFS analysis do not allow such work but there are methods that can be employed. At the stand level (20-50 acres) the computer programs NEXUS or Fuels Management Analyst (FMAPlus ) can be used to compare the crown fire performance of different treatments. At the watershed scale FARSITE and/or FLAMMAP can be used to test different spatial arrangements of treatments and how they will impact wildfire severity and size. FARSITE will also allow for suppression modeling to determine if fuel treatments will improve suppression efficiency.
To reduce potential fire behavior at the landscape scale will require partnerships with private industry. Infrastructure such as biomass utilization plants and sawmills are part of the solution. Without this infrastructure the current fire hazard problems would be much more difficult to solve.

The forests in the Sierra Nevada and Southern Cascades have diverse ownerships. To produce effective landscape fire behavior strategies will require the cooperation of federal, state, and private land owners. If the USFS only treats their land without coordination and cooperation of the other land owners, the overall strategy will not meet the desired objective.

Urban-Wildland Intermix

Land management agencies throughout the country are increasingly aware of the difficulties of managing in the urban-wildland intermix. This is a very complicated landscape with homes, subdivisions, and towns all mixed into or adjoining wildland areas. The number of people who choose to live in this area continues to increase and many wildland fire agencies such as the California Department of Forestry and Fire Protection, believe this is the area where their fuels treatments should be focused.

I believe this area requires partnerships between home owners and the public or private groups that have responsibility for the adjoining wildlands. DFPZ’s can be created in the urban wildland intermix to allow for more effective and safe suppression activities when wildfires are moving from the wildlands toward homes or from the homes into the wildlands.

Private home owners share responsibility in this area. Homes must be built with combustion resistant roofs and siding materials. Defensible space must be created around each structure to increase the probability that it will survive a wildfire. Fine fuels and needles must be removed annually from roofs and around houses to reduce the chance of spot fire ignition during wildfires. To be successful in this area, a shared partnership must occur between the private land owners and managers of the adjoining wildlands. Currently most of the debate is focusing on what large land managers must do to reduce risk but an equal amount of responsibility rests on the private side of the intermix. Counties and states must take action to ensure that individual home owners reduce their potential for catastrophic fire. To date, most of the counties in the Sierra Nevada and Southern Cascades have not addressed this absolutely critical issue. This is beyond the scope of the current USFS plan but it is a critical step in this process.

Implementation Strategy, Monitoring, and Adaptive Management

There presently is a diversity of opinions between environmental groups, commodity interest groups, the State, and others, on what actually should be done to reduce potential fire behavior in federal forests in this region. Mechanisms should be created to encourage participants to interact and reach agreements. Principles that can assist in this interaction include 1) locate projects in areas with substantial agreement on restoration objectives, 2) reflect and celebrate accomplishments in order to build relationships, trust, and support, 3) create an extensive, well designed adaptive management program to learn from management actions, and 4) create an all party monitoring process to assure credible post-treatment data and analysis. The monitoring and evaluation program should be directed by a non-federal group to ensure independence.

My present position as a fire science professor at the University of California, Berkeley, has introduced me to many different groups and people that are incredibly engaged in the this region. I have met with hundreds of people over the last 2 years in reference to the Sierra Nevada and Southern Cascades, and I believe a comprehensive strategy must be developed by which a decision can be implemented.

I believe the USFS should choose 3 areas of National Forest lands from this region to begin work outlined in the final modified decision. If properly designed, the 3 areas could allow for a broad discussion on the effects of different fuel treatments with a diverse group of people. This group could include environmental groups, commodity use groups, forest service staff, state of California personal, university and federal scientists, and the public. The main objective of the monitoring and evaluation will be to determine if the fire and wildlife habitat goals were obtained.

The size of each area should be relatively large (possibly several sub-watersheds, an area of approximately 50,000-100,000 acres). One could be place in the southern, central, and northern areas that this plan addresses. Since we have almost no information on the effects of fire hazard treatments on any aspect of the ecosystem, these areas can be used to develop an information base for future work. I think it is essential that scientists from the University of California (Berkeley and Davis campuses) be included in such a program along with the California Department of Forestry and Fire Protection and the USFS Pacific Southwest Research Station. The existing California Cooperative Ecosystem Science Unit could facilitate this partnership between the USFS and the University of California. The monitoring and evaluation program should be headed by a non-federal agency and this would benefit the USFS.

The present Administrative Study in the Quincy Library Group (QLG) area could provide some of this information but the selection and layout of the treatment areas would have to be modified to accommodate this goal. Presently the activities planned focus on DFPZ’s and group selection. At a minimum, it should be changed to include SPLAT’s without any DFPZ’s or groups in some of the Treatment Units. We must learn how effective SPLAT’s and DFPZ’s are and what changes to key ecosystem processes occur with their installation and maintenance.

There currently exists tremendous variability in forest structure within the federal lands of the Sierra Nevada and Southern Cascades. With such diverse current conditions it is impossible to produce one methodology to restore and sustain all of these areas. Prescribed fire is one very important tool that land managers can use to reduce potential fire behavior and increase sustainability. Mechanical methods coupled with prescribed fire are another effective method in reducing potential fire behavior. Carefully designed mechanical methods may also be effective in reducing potential fire behavior but they will not be successful in simulating the full ecosystem processes of fire, and should probably be limited in their spatial extent. We need a diverse set of tools to design ground-based treatments to restore and maintain the vast forests in this region. All treatments that manipulate vegetation must evaluate their impacts on potential fire behavior.

The final plan must include the fiscal commitments necessary to support adaptive management and monitoring. The present plan comes up very short in this important area. It essentially says that we have the answer to the present problems and now we are going to implement it at very large spatial scales. Unfortunately, I think this is a prescription for more fighting and lawsuits. Using an approach where everyone that chose to engage in the process could be a partner and learn would be a much better approach. Adaptive management and all party monitoring is a key step in this process.

Thank you for the opportunity to speak.

February 19, 2004

Scientists Move Closer to Identifying World's Oldest Asexual Organism

by Kathryn Stelljes

BERKELEY - New findings about ancient fungi provide a key to resolving a basic mystery of evolution and may lead to improved agricultural production, according to University of California, Berkeley, scientists.

Biologists believe that sexual reproduction is essential to long-term survival of species, and only a very few species are thought to have survived for long periods without sex. Arbuscular mycorrhizal (AM) fungi, which colonize roots of most land plants and improve both their ability to obtain nutrients and to tolerate disease, may be the group of organisms that has done so. No one has found any sex organs in these fungi, and their 460-million-year-old fossils, from the Ordovician period, look just like modern species.

If these fungi truly are asexual, the age of the oldest known asexual organism would be pushed back by a factor to 10. A group of rotifers currently is the oldest known asexual organism.

Until now, however, tests for asexuality could not be applied to AM fungi because it was thought that they contained many different nuclei in each cell.

In this week's issue of the journal Nature, new evidence by UC Berkeley biologists Teresa Pawlowska and John Taylor shows that the nuclei in AM fungi are identical - information that will allow the tests of asexuality to proceed.

The team used genetics to study inheritance in spores and molecular biology to study genetic variation in individual nuclei to show that each nucleus was just like the others.

"The two challenges that we faced were that AM fungi must be grown with a plant and that there is very little DNA in a single nucleus," said postdoctoral researcher Pawlowska, lead author on the paper. Both she and Taylor are in the Department of Plant and Microbial Biology in the campus's College of Natural Resources.

In addition to the inherent biological interest in the fungi, understanding the life cycle of AM fungi could have agricultural applications. By benefiting plant nutrition and disease resistance, AM fungi provide an alternative to chemical fertilizers, particularly in land reclamation, habitat restoration and sustainable agriculture. Popular interest in organically grown foods has precipitated an explosion of companies that produce and market soil amendments containing AM fungi, currently a $10 million industry worldwide. Yet, scientific development of these products and their evaluation had been hampered by a lack of understanding of the genetics of AM fungi.

"To evaluate the effectiveness of these products, and to develop improved soil amendments, we need to know how AM fungi reproduce," said Pawlowska. "These findings allow us to move forward."

This project was made possible by funding from Syngenta (formerly Novartis) through a grant to UC Berkeley's plant and microbial biology department. Initial results obtained during the Syngenta-funded project then led to grant support from the U.S. Department of Agriculture's competitive grants program.

February 10, 2004

Bighorn Sheep Threatened by Climate Change


by Sarah Yang

BERKELEY – A study led by researchers at the University of California, Berkeley, has linked population declines of California's desert bighorn sheep with the effects of climate change. What's more, many of the state's remaining bighorn populations could face extinction if certain global warming forecasts for the next 60 years come true.

In the study, which is published in the current issue of Conservation Biology, the authors found that of the 80 groups of desert bighorn sheep known to have roamed California's mountains over the past century, 30 are now extinct.

In their investigation of the population decline, the researchers evaluated impacts ranging from contact with domestic livestock, which can lead to the spread of disease and competition for food, to poaching, mining, human disturbance and other factors. They also analyzed climatic variables such as temperature and precipitation that affect the availability of vegetation and dependable sources of spring water for the sheep.

"Climate was consistently correlated with extinction in a way the other factors weren't," said Clinton W. Epps, a doctoral student in environmental science, policy and management at UC Berkeley's College of Natural Resources and lead author of the paper. "The harsh environment inhabited by desert bighorn sheep already has them walking on a knife's edge. It doesn't take too much to push them off. The bottom line is that more than one-third of the populations that were once known are now gone," said Epps.

From 1901 to 1987, the mean annual temperature in the deserts of the southwestern United States increased by about 1.8 degrees Fahrenheit, which is considered significant by climatologists. In addition, annual precipitation dropped about 20 percent in southeastern California over the last century. According to the study, groups of bighorn sheep were more likely to be lost in lower elevation mountains where there were higher average temperatures and less precipitation.

The authors examined population data on the state's desert bighorn sheep, or Ovis canadensis nelsoni, collected since 1940 by biologists and California Department of Fish and Game researchers. They also used historical records from local areas where the sheep were known to have lived, but had since disappeared.

Desert bighorn sheep primarily live in small, isolated groups throughout the mountain ranges of the Sonoran, Mojave and Great Basin deserts of the southwestern United States. In southwestern California, they are also found in the Transverse and Peninsular mountain ranges.

Bighorn has been a species of concern among conservationists since they were first protected by California legislation in 1873. Statewide, the population of desert bighorn is estimated at 3,500. Bighorn in the Peninsular and Sierra Nevada mountain ranges are listed as state and federal endangered species.

"When you start losing bighorn sheep from some mountain ranges, it affects the collective population," said Dale R. McCullough, professor of ecosystem sciences at UC Berkeley's College of Natural Resources and co-author of the paper. "Any decline in vegetation makes it more difficult for sheep to move among the different habitat clusters, which have become fewer and more spread out. Where they used to be able to move more readily to other mountain ranges to help repopulate or recolonize a habitat area, they must now cross an intervening desert."

McCullough noted that effects on populations from global warming are easier to detect in bighorn sheep than species of other large mammals that are more uniformly distributed over the landscape. "Other large mammals may shift north more gradually as a result of global warming, but that trend is harder to detect in the short term," he said.

The authors also looked at predictions of how climate may change in the next 60 years. For scenarios that predict a minimum temperature increase of 1.3 degrees Fahrenheit, there is no significant increase in the average probability of extinction. However, in scenarios that predict a more serious temperature increase of 3.6 degrees Fahrenheit and a 12 percent decrease in precipitation, the probability of extinction increases significantly from a baseline of 20 percent to 30 percent in the next 60 years.

Epps points out that this increase is an average of the extinction probability calculated for each group remaining in southern California. The risks for some individual groups, particularly those that live at lower elevations, are significantly higher.

"Our study illustrates how sensitive certain populations can be to changes in climate, whether man-made or not," said Epps. "Cases like this give conservationists some ammunition when talking about the importance of controlling global warming."

Other co-authors of the study are John D. Wehausen of the White Mountain Research Station, Vernon C. Bleich of the California Department of Fish and Game, and Jennifer L. Rechel of the U.S. Forest Service.

February 2, 2004

Scientists Obtain First Genomes of Microbes Directly from Environment

by Robert Sanders

Berkeley - In the first triumph of a field dubbed "environmental genomics," scientists at the University of California, Berkeley, in collaboration with the Joint Genome Institute, have for the first time sequenced the genomes of the most abundant members of a community of organisms - not one at a time, but simultaneously.

The researchers took a simple community of microbes from a pink slick on the floor of an abandoned mine, ground them up, and shotgun sequenced the lot. As they put the pieces of DNA back together, the snippets fell easily into five distinct genomes, four of them unknown until now.

"This is the first recovery of a genome from an environmental sample," said Jillian F. Banfield, professor of earth and planetary science and of environmental science, policy and management at UC Berkeley. "This ushers in a whole new way of exploring and understanding our environment, allowing us to determine how organisms work as individuals and together, and how they contribute to geochemical processes."

Banfield and graduate student Gene W. Tyson from UC Berkeley's Department of Environmental Science, Policy and Management, with colleagues from UC Berkeley and the U.S. Department of Energy's Joint Genome Institute (JGI) in Walnut Creek, Calif., report their feat this week in the Advance Online Publication of the journal Nature.

Banfield and her students, post docs and colleagues are primarily interested in how the microbes, obtained from the Richmond Mine in Iron Mountain, Calif., one of the largest Superfund sites in the country, interact with minerals to produce acid mine drainage.

"Acid mine drainage is one of the most pressing long-term environmental problems worldwide, and it's caused by microbial processes," Banfield said. "This study has dramatically improved our understanding of the microorganisms involved and has opened the way for development of much more highly refined models of acid mine drainage systems."

"If we understand the organisms and how they cause this environmental problem, we can try to do something about it in the long run," Tyson added.

"This represents an important example of how the production sequencing capacity developed by the Department of Energy at the JGI for the human genome program can provide fundamental insights into vital environmental problems," said JGI Director Eddy Rubin.

Understanding the biofilm ecosystem also may be relevant to the search for life on Mars, since it's conceivable that the iron and sulfur-rich surface of Mars could harbor microbes that eat iron, similar to those in iron and sulfur-rich pyrite mines like the Richmond Mine.

For the past nine years, Banfield has been studying a pink microbial biofilm that sits like scum on the surface of green pools of water, as acidic as battery acid, in the dark depths of the Richmond Mine, located nine miles northwest of Redding. Her goal is to understand how the extremophiles - microbes that live in extreme environments - live together and generate the acid drainage that makes such mines toxic hazards. The green runoff from the mine, captured and treated by the Environmental Protection Agency, is not only acidic, but also contains high levels of toxic metals - zinc, iron, copper and arsenic - and is a piping 108 degrees Fahrenheit.

In this low-light, low-oxygen, high-acid and toxic environment about 1,400 feet into the mountain, the microbes thrive. They fix carbon and nitrogen from the carbon dioxide and nitrogen in the air, eat iron by oxidizing it with oxygen, and in the process dissolve the iron pyrite (iron sulfide, also known as fool's gold) to create sulfuric acid.

Previously, researchers have studied microbial communities, such as those in hot springs or in the ocean, either by isolating individual organisms or strains, culturing them and sequencing the cultured population; or by plucking bits and pieces of genes from the various members of the community.

A big problem is that only about one in 100 microbes can be cultured sufficiently to extract its genome. Even if a microbial genome is known, however, this still doesn't tell researchers how it interacts with other microbes in its environment.

Banfield and other researchers have been looking at a more daring approach - sequencing the whole community at once, a technique Banfield prefers to call "community genomics." That's like surveying the species in the African veldt by grinding up lions, zebras, elephants and an unknown number of other animals, cutting the genes into tiny pieces, and trying to sort them into distinct genomes.

But it works, Banfield said, "at least with the small number of distinct organisms in this community."

"The magic of the whole thing is that, because of speciation, these organisms are different enough that their genomes are easy to tell apart," Banfield said. The technique would allow researchers to sequence the genomes of microbes that cannot be raised in isolated cultures.

Banfield's group and the group at the JGI reassembled the genomes, each containing about 2,000 genes, using different software programs to arrive at composite genomes. Two of the draft genomes - for a Leptospirillum group II bacterium and a Ferroplasma type II microbe from the ancient group known as Archaea - are now about 97 percent complete, with a few gaps. The genome of one of the six microbes in the community, Ferroplasma acidarmanus (a type I Ferroplasma), had been sequenced earlier by JGI and Banfield's group and was a good control during the sequencing and assembly process.

The other genomes were highly fragmented, but identifiable as microbes from Leptospirillum group III, Ferroplasma type I and a G-plasma microbe.

"Despite the highly fragmented nature of three of the genomes, we had enough coverage and many, many genes to get an idea of what the organisms do in the environment," Tyson said.

The genome of Leptospirillum group II is the first sequenced from the phylum Nitrospira, an important branch of the tree of life containing nitrate and nitrogen cycling bacteria, Banfield noted.

Once Banfield's group had the five new genomes, they compared the genes in each with a database of known genes to identify their functions. For the two microbes with the most complete draft genomes, they were able to reconstruct nearly the entire metabolic cycle.

Already they have determined how the microbes share tasks in the isolated microbial community of the mine. The Leptospirillum group II bacteria fix carbon and produce the biofilm that protects them and keeps them afloat, while a minor member of the community, Leptospirillum group III bacteria, fix both carbon and nitrogen. The iron is probably munched by the all of the biofilm members, including Ferroplasma microbes.

Interestingly, the Ferroplasma type II microbes in the biofilm apparently are a mix of many different strains, but the genome reconstruction shows that they all arose from three distinct ancestral strains. Random sex among the microbes for millions of years has combined and recombined the genomes of the three strains so that the population today consists of strains that mix and match genes from separate ancestors.

"This type of rampant exchange of genetic material has never been documented in Archaea or in natural samples before," Banfield said. "This recombination may be a strategy for maintaining optimization in the event of perturbations in the environment. The observation helps us understand the factors that shape evolution and drive development of new species."

Banfield said that the community genome technique worked in this situation because the dominant microbes were represented mostly by closely related strains. In more complex environments with more organisms, it may not be so easy.

"However, even in more complex environments it should be possible to extend the random shotgun sequencing approach to recover genomes of uncultivated strains and species," the authors wrote. "These data can then be used to explore the nature of the community metabolic network, to find conditions for cultivating previously uncultivated organisms, to monitor community structure over time, and to construct DNA microarrays to monitor global community gene expression patterns."

While the current study provides a wealth of information about the five microbes, it's only the beginning for the team. With the genes in hand, they plan to create microarrays - so-called gene chips - to determine how gene expression and protein production change with changing conditions in the microbial community. For example, as the acidity or temperature changes, how do the organisms react? How do they change their carbon or nitrogen fixation, or their scavenging of iron from the acidic groundwater?

"The next step in this project is to get whole community genome arrays up and running to look at these organisms and how they respond to certain conditions," Tyson said.

Other authors include Edward Rubin, Paul Richardson and Victor Solovyev of the Joint Genome Institute; Daniel Rokhsar and Jarrod Chapman of both JGI and UC Berkeley's Department of Physics; and graduate students Philip Hugenholtz, Eric E. Allen and Rachna J. Ram of UC Berkeley's Department of Environmental Science, Policy and Management.

This research was funded by the US Department of Energy's Office of Science and the National Science Foundation's Biocomplexity Program.


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Stephens Testifies on Sierra Nevada Forest Plan
Scientists Move Closer to Identifying World's Oldest Asexual Organism
Bighorn Sheep Threatened by Climate Change
Scientists Obtain First Genomes of Microbes Directly from Environment


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