1. Faced with widespread degradation of riverine ecosystems, stream restoration has greatly increased. Such restoration is rarely planned and executed with inputs from ecological theory. In this paper, we seek to identify principles from ecological theory that have been, or could be, used to guide stream restoration. 2. In attempts to re-establish populations, knowledge of the species' life history, habitat template and spatio-temporal scope is critical. In many cases dispersal will be a critical process in maintaining viable populations at the landscape scale, and special attention should be given to the unique geometry of stream systems 3. One way by which organisms survive natural disturbances is by the use of refugia, many forms of which may have been lost with degradation. Restoring refugia may therefore be critical to survival of target populations, particularly in facilitating resilience to ongoing anthropogenic disturbance regimes. 4. Restoring connectivity, especially longitudinal connectivity, has been a major restoration goal. In restoring lateral connectivity there has been an increasing awareness of the riparian zone as a critical transition zone between streams and their catchments. 5. Increased knowledge of food web structure - bottom-up versus top-down control, trophic cascades and subsidies - are yet to be applied to stream restoration efforts. 6. In restoration, species are drawn from the regional species pool. Having overcome dispersal and environmental constraints (filters), species persistence may be governed by local internal dynamics, which are referred to as assembly rules. 7. While restoration projects often define goals and endpoints, the succession pathways and mechanisms (e.g. facilitation) by which these may be achieved are rarely considered. This occurs in spite of a large of body of general theory on which to draw. 8. Stream restoration has neglected ecosystem processes. The concept that increasing biodiversity increases ecosystem functioning is very relevant to stream restoration. Whether biodiversity affects ecosystem processes, such as decomposition, in streams is equivocal. 9. Considering the spatial scale of restoration projects is critical to success. Success is more likely with large-scale projects, but they will often be infeasible in terms of the available resources and conflicts of interest. Small-scale restoration may remedy specific problems. In general, restoration should occur at the appropriate spatial scale such that restoration is not reversed by the prevailing disturbance regime. 10. The effectiveness and predictability of stream ecosystem restoration will improve with an increased understanding of the processes by which ecosystems develop and are maintained. Ideas from general ecological theory can clearly be better incorporated into stream restoration projects. This will provide a twofold benefit in providing an opportunity both to improve restoration outcomes and to test ecological theory.

Linking ecological theory with stream restoration

During the cycling of seawater through the earth9s crust along the mid-ocean ridge system, geothermal energy is transferred into chemical energy in the form of reduced inorganic compounds. These compounds are derived from the reaction of seawater with crustal rocks at high temperatures and are emitted from warm (≤25°C) and hot (∼350°C) submarine vents at depths of 2000 to 3000 meters. Chemolithotrophic bacteria use these reduced chemical species as sources of energy for the reduction of carbon dioxide (assimilation) to organic carbon. These bacteria form the base of the food chain, which permits copious populations of certain specifically adapted invertebrates to grow in the immediate vicinity of the vents. Such highly prolific, although narrowly localized, deep-sea communities are thus maintained primarily by terrestrial rather than by solar energy. Reduced sulfur compounds appear to represent the major electron donors for aerobic microbial metabolism, but methane-, hydrogen-, iron-, and manganese-oxidizing bacteria have also been found. Methanogenic, sulfur-respiring, and extremely thermophilic isolates carry out anaerobic chemosynthesis. Bacteria grow most abundantly in the shallow crust where upwelling hot, reducing hydrothermal fluid mixes with downwelling cold, oxygenated seawater. The predominant production of biomass, however, is the result of symbiotic associations between chemolithotrophic bacteria and certain invertebrates, which have also been found as fossils in Cretaceous sulfide ores of ophiolite deposits.

https://science.sciencemag.org/content/sci/229/4715/717.full.pdf

Geomicrobiology of Deep-Sea Hydrothermal Vents

A new extremely thermophilic methane-producing bacterium was isolated from a submarine hydrothermal vent sample collected by a research team from the Woods Hole Oceanographic Institution using the manned submersible ALVIN. The sample was obtained from the base of a “white smoker” chimney on the East Pacific Rise at 20° 50′ N latitude and 109° 06′ W longitude at a depth of 2600 m. The isolate was a motile irregular coccus with an osmotically fragile cell wall and a complex flagellar system. In defined medium with 80% H2 and 20% CO2, the isolate had a doubling time of 26 min at 85° C. The pH range for growth was 5.2 to 7.0 with an optimum near 6.0. NaCl was required for growth with an optimum of 2 to 3% (w/v). The mol % G+C was 31%. In cell-free extracts, methane formation from methylcoenzyme M was temperature-dependent, and H2 or formate served as electron donors. Methane formation from H2 and CO2 occurred at a much lower rate. Oligonucleotide cataloging of the 16S ribosomal RNA established the isolate as a new species of the genus Methanococcus and the name Methanococcus jannaschii is proposed. The isolation of M. jannaschii from a submarine hydrothermal vent provides additional evidence for biogenic production of CH4 from these deep-sea environments.

Methanococcus jannaschii sp. nov., an extremely thermophilic methanogen from a submarine hydrothermal vent

Organisms capable of autotrophic metabolism assimilate inorganic carbon into organic carbon. They form an integral part of ecosystems by making an otherwise unavailable form of carbon available to other organisms, a central component of the global carbon cycle. For many years, the doctrine prevailed that the Calvin-Benson-Bassham (CBB) cycle is the only biochemical autotrophic CO2 fixation pathway of significance in the ocean. However, ecological, biochemical, and genomic studies carried out over the last decade have not only elucidated new pathways but also shown that autotrophic carbon fixation via pathways other than the CBB cycle can be significant. This has ramifications for our understanding of the carbon cycle and energy flow in the ocean. Here, we review the recent discoveries in the field of autotrophic carbon fixation, including the biochemistry and evolution of the different pathways, as well as their ecological relevance in various oceanic ecosystems.

Beyond the Calvin cycle: autotrophic carbon fixation in the ocean.

Submarine hydrothermal vents are the only comtemporary geological environment which may be called truly primeval; they continue to be a major source of gases and dissolved elements to the modern ocean as they were to the Archean ocean. Then, as now, they encompassed a multiplicity of physical and chemical gradients as a direct result of interactions between extensive hydrothermal activity in the Earth's crust and the overlying oceanic and atmospheric environments. We have proposed that these gradients provided the necessary multiple pathways for the abiotic synthesis of chemical compounds, origin and evolution of ‘precells’ and ‘precell’ communities and, ultimately, the evolution of free-living organisms. This hypothesis is consistent with the tectonic, paleontological, and degassing history of the earth and with the use of thermal energy sources in the laboratory to synthesize amino acids and complex organic compounds. In this paper, we expand upon the geophysical, chemical, and possible microbiological analogies between contemporary and Archean hydrothermal systems and suggest several hypotheses, related to our model for the origin and evolution of life at Archean vents, which can be tested in present-day hydrothermal systems.

Submarine hydrothermal vents and associated gradient environments as sites for the origin and evolution of life

Submarine hydrothermal vents are a major source of methane to the oceans1,2 The methane, as well as H2 and CO, are generally believed to result from degassing of the mantle or from abiogenic water–rock reactions1, a conclusion supported by direct correlations between 3He and CH4, and generally between CH4, H2 and CO and dissolved silicate in hydrothermal waters2,3 An alternative source for these gases might be microbiological This would imply that active bacterial communities exist in deep-sea hot water environments, some of which have temperatures exceeding 100 °C; this inference is without precedent We have now found that the super-heated waters emanating from sulphide chimneys at 21 °N along the East Pacific Rise and samples from the sulphide chimneys themselves harbour complex communities of bacteria capable of growing with generation times of 37–65 min, producing CH4, CO, H2 and traces of N2O in media containing S2O2−3, Mn2+ and Fe2+ as energy sources, and oxidizing CH4, at 100 ± 2 °C at 1 atm These microbial communities consist of three to five morphologically distinct types and include both oxidative and anaerobic species These mixed cultures will not grow at temperatures below 70–75 °C Even though some of the communities originated from water of temperatures >300 °C, it is not known if they can grow and produce CH4, CO and H2 in super-heated waters kept liquid due to hydrostatic pressure The discovery of these obligately thermophilic, gas-producing and consuming bacterial communities associated with submarine volcanic environments has interesting and important implications for prokaryotic evolution, marine geochemistry, industrial microbiology and exobiology

Is the CH 4 , H 2 and CO venting from submarine hydrothermal systems produced by thermophilic bacteria?

Hydrothermal fluids at the Galapagos Spreading Center (GSC) and at 21°N on the East Pacific Rise were enriched in methane, hydrogen and carbon monoxide by orders of magnitude over ambient bottom water. Nitrous oxide showed both enrichment and depletion in warm vent waters. Each GSC vent field exhibited unique dissolved gas to silica ratios indicating that complex source — sink mechanisms operated within a small geographic region. The CH4/3 He ratio at 21°N was 6.1 × 106 whereas at the GSC, a range of 12.4 to 42 × 106 was seen. At 21°N the H2/3 He ratio was on the order of 100 times that at the GSC. Microbial data showed as many as 109 organisms ml−1 in GSC samples and 105 ml−1 in the hot 21°N waters. These microbial communities are complex and include organisms known to produce and consume the gases discussed here. We conclude that microbial activity in the warm GSC vents is a significant contributing factor in determining the final gas concentrations in the vent waters.

Reduced Gases and Bacteria in Hydrothermal Fluids: The Galapagos Spreading Center and 21°N East Pacific Rise

Hydrogen, methane, and relevant microbiological and hydrographic observations were made to study the processes responsible for the observed distributions of the gases in Saanich Inlet, a seasonally anoxic fjord. Concentrations of surface waters were up to 22 (H2) and 13 (CH4) times atmospheric saturation. Below the surface hydrogen fell to undersaturation, rising to above saturation in the anoxic layer. Methane increased to a maximum at 30 m, and after a minimum at 125 m, increased greatly in the anoxic layer. Microbes cultured from inlet surface water produced hydrogen under experimental conditions, not by nitrogen fixation but while apparently denitrifying. Large numbers of protozoa present may provide anaerobic microniches for hydrogen and methane production, as might the intestinal tracts of the large populations of higher organisms in the inlet. Methane profiles in the upper 50 m are typical of waters outside the inlet, indicating regional sources and sinks. Hydrogen production and consumption rates, inferred to be rapid in the anoxic waters, nearly balance so that only slight increases in hydrogen occur there.

Dissolved hydrogen and methane in Saanich Inlet, British Columbia

Hydrothermal circulation systems of mid-ocean ridges profoundly influence the chemistry of the oceans and the oceanic crust1–3. This has been demonstrated for several major and minor constituents of seawater4 and trace metals5. In addition, several volatile compounds including helium6,7 as well as methane and hydrogen8–11 are introduced to the sea floor in concentrations greatly exceeding that of ambient bottom water. We present here our measurements of concentrations of methane, hydrogen, carbon monoxide and nitrous oxide in the hydrothermal vent waters from the Galapagos Spreading Centre (GSC). The relationships of these constituents to silicon were unique for each vent field, with nitrous oxide at East of Eden being the only instance of negative correlation. These gases could serve as important energy sources, in addition to hydrogen sulphide, for the chemosynthetic bacteria which support the extensive and diverse animal population living in these environments12,13.

CH 4 , H 2 , CO and N 2 O in submarine hydrothermal vent waters

No published reports exist on the early stages in the establishment and succession of microbial communities and associated chemical and geochemical transformations in aquatic environments shortly after a volcanic event. Much of our understanding of volcanic lakes has come from studies carried out years to centuries after the eruption, when the lakes were already stabilized. Here we document the chemical and microbiological responses of lakes and hydrothermal environments in the blast zone near Mt St Helens 3–4 months after the eruption of 18 May 1980. Within weeks of the eruption, the impacted lakes became anaerobic, ultraeutrophic and developed extensive populations of bacteria, some of which were not common to those environments. By August 1980 both assimilative and dissimilative nitrogen cycle reactions were regulating the extent of chemosynthetic, photosynthetic and heterotrophic activities occurring in the lakes. Recovery of the lakes to their normal oligotrophic state will result in part from oxygen production by photosynthesis and anaerobic oxidation of reduced metals, gases and organic compounds coupled with denitrification.

Marvin D. Lilley

Papers

Is the CH 4 , H 2 and CO venting from submarine hydrothermal systems produced by thermophilic bacteria?

Reduced Gases and Bacteria in Hydrothermal Fluids: The Galapagos Spreading Center and 21°N East Pacific Rise

Dissolved hydrogen and methane in Saanich Inlet, British Columbia

CH 4 , H 2 , CO and N 2 O in submarine hydrothermal vent waters

Initial microbiological response in lakes to the Mt St Helens eruption