Bamboo as bioresource in Ethiopia: management strategy to improve seedling performance (Oxytenanthera abyssinica)

Seedling emergence and subsequent survival and growth are vital for natural forest restoration or plantation establishment by means of seeds. Such information is lacking for the African bamboo species. Two experiments were carried out in a greenhouse to evaluate the influence of seed orientation and sowing depth of the lowland bamboo Oxytenanthera abyssinica on seedling emergence, survival and growth. A randomised complete block design was used. Seedling emergence in the seed orientation experiment followed the order embryo-end-up>lay-flat>embryo-end-down. Survival rate after 62 days decreased in the order lay-flat>embryo-end-down>embryo-end-up. Mean seedling height and number of leaves per seedling followed a similar pattern. Seeds sown on top of the soil surface and at 2.5 mm depth achieved faster and higher seedling emergence than those sown at 5 and 10 mm depths. However, mean seedling height and number of leaves per seedling were higher in 5 and 2.5 mm depths than surface and 10 mm depths. There were significant quadratic relationships between sowing depth and seedling height (p=0.034) as well as number of leaves per seedling (p=0.032), both peaking around 5 mm soil depth. Lay-flat orientation, which is the most frequent position in broadcast sowing, is recommended at 5 mm sowing depth for the lowland bamboo based on overall performance in seedling emergence, survival and growth.     

Characterization and spatial distribution of methanogens and methanogenic biosignatures in hypersaline microbial mats of Baja California

Well-developed hypersaline cyanobacterial mats from Guerrero Negro, Baja California Sur, sustain active methanogenesis in the presence of high rates of sulfate reduction. Very little is known about the diversity and distribution of the microorganisms responsible for methane production in these unique ecosystems. Applying a combination of 16S rRNA and metabolic gene surveys, fluorescence in situ hybridization, and lipid biomarker analysis, we characterized the diversity and spatial relationships of methanogens and other archaea in the mat incubation experiments stimulated with methanogenic substrates. The phylogenetic and chemotaxonomic diversity established within mat microcosms was compared with the archaeal diversity and lipid biomarker profiles associated with different depth horizons in the in situ mat. Both archaeal 16S rRNA and methyl coenzyme M reductase gene (mcrA) analysis revealed an enrichment of diverse methanogens belonging to the Methanosarcinales in response to trimethylamine addition. Corresponding with DNA-based detection methods, an increase in lipid biomarkers commonly synthesized by methanogenic archaea was observed, including archaeol and sn-2-hydroxyarchaeol polar lipids, and the free, irregular acyclic isoprenoids, 2,6,10,15,19-pentamethylicosene (PMI) and 2,6,11,15-tetramethylhexadecane (crocetane). Hydrogen enrichment of a novel putative archaeal polar C(30) isoprenoid, a dehydrosqualane, was also documented. Both DNA and lipid biomarker evidence indicate a shift in the dominant methanogenic genera corresponding with depth in the mat. Specifically, incubations of surface layers near the photic zone predominantly supported Methanolobus spp. and PMI, while Methanococcoides and hydroxyarchaeol were preferentially recovered from microcosms of unconsolidated sediments underlying the mat. Together, this work supports the existence of small but robust methylotrophic methanogen assemblages that are vertically stratified within the benthic hypersaline mat and can be distinguished by both their DNA signatures and unique isoprenoid biomarkers.     

Evolutionary innovation: a bone-eating marine symbiosis

Symbiotic associations between microbes and invertebrates have resulted in some of the most unusual physiological and morphological adaptations that have evolved in the animal world. We document a new symbiosis between marine polychaetes of the genus Osedax and members of the bacterial group Oceanospirillales, known for heterotrophic degradation of complex organic compounds. These organisms were discovered living on the carcass of a grey whale at 2891 m depth in Monterey Canyon, off the coast of California. The mouthless and gutless worms are unique in their morphological specializations used to obtain nutrition from decomposing mammalian bones. Adult worms possess elaborate posterior root-like extensions that invade whale bone and contain bacteriocytes that house intracellular symbionts. Stable isotopes and fatty acid analyses suggest that these unusual endosymbionts are likely responsible for the nutrition of this locally abundant and reproductively prolific deep-sea worm.     

Lipid biomarker and carbon isotopic signatures for stromatolite-forming, microbial mat communities and Phormidium cultures from Yellowstone National Park

The molecular and isotopic compositions of lipid biomarkers from cultured filamentous cyanobacteria (Phormidium, also known as Leptolyngbya) have been used to investigate the community and trophic structure of photosynthetic mats from alkaline hot springs of the Lower Geyser Basin at Yellowstone National Park. We studied a shallow‐water coniform mat from Octopus Spring (OS) and a submerged, tufted mat from Fountain Paint Pots (FPP) and found that 2‐methylhopanepolyols and mid‐chain branched methylalkanes were diagnostic for cyanobacteria, whereas abundant wax esters were representative of the green non‐sulphur bacterial population. The biomarker composition of cultured Phormidium‐isolates varied, but was generally representative of the bulk mat composition. The carbon isotopic fractionation for biomass relative to dissolved inorganic carbon (DIC; ?_CO2) for cultures grown with 1% CO₂ ranged from 21.4 to 26.1 and was attenuated by diffusion limitation associated with filament aggregation (i.e. cell clumping). Isotopic differences between biomass and lipid biomarkers, and between lipid classes, depended on the cyanobacterial strain, but was positively correlated with overall fractionation. Acetogenic lipids (alkanes and fatty acids) were generally more depleted than isoprenoids (phytol and hopanoids). The δ¹³C_TOC for OS and FPP mats were somewhat heavier than for cultures (?16.9 and ?23.6, respectively), which presumably reflects the lower availability of DIC in the natural environment. The isotopic dispersions among cyanobacterial biomarkers, biomass and DIC reflected those established for culture experiments. The 7‐methyl‐ and 7,11‐dimethylheptadecanes were from 9 to 11 depleted relative to the bulk organic carbon, whereas 2‐methylhopanols derived from the oxidation‐reduction of bacteriohopanepolyol were enriched relative to branched alkanes by approximately 5–7. These isotopic relationships survived with depth and indicated that the relatively heavy isotopic composition of the OS mat resulted from diffusion limitation. This study supports the suggestion that culture studies can establish valid isotopic relationships for interpretation of trophic structure in modern and ancient microbial ecosystems.     

Lipid biomarker and phylogenetic analyses to reveal archaeal biodiversity and distribution in hypersaline microbial mat and underlying sediment

This study has utilized the tools of lipid biomarker chemistry and molecular phylogenetic analyses to assess the archaeal contribution to diversity and abundance within a microbial mat and underlying sediment from a hypersaline lagoon in Baja California. Based on abundance of ether-linked isoprenoids, archaea made up from 1 to 4% of the cell numbers throughout the upper 100 mm of mat and sediment core. Below this depth archaeal lipid was two times more abundant than bacterial. Archaeol was the primary archaeal lipid in all layers. Relatively small amounts of caldarchaeol (dibiphytanyl glyceroltetraether) were present at most depths with phytanyl to biphytanyl molar ratios lowest (~10 : 1) in the 4–17 mm and 100–130 mm horizons, and highest (132 : 1) in the surface 0–2 mm. Lipids with cyclic biphytanyl cores were only detected below 100 mm. A novel polar lipid containing a C₃₀ isoprenoid (squalane) moiety was isolated from the upper anoxic portion of the core and partially characterized. Hydrocarbon biomarker lipids included pentamethylicosane (2–10 mm) and crocetane (primarily below 10 mm). Archaeal molecular diversity varied somewhat with depth. With the exception of samples at 0–2 mm and 35–65 mm, Thermoplasmatales of marine benthic group D dominated clone libraries. A significant number of phylotypes representing the Crenarchaeota from marine benthic group B were generally present below 17 mm and dominated the 35–65 mm sample. Halobacteriaceae family made up 80% of the clone library of the surface 2 mm, and consisted primarily of sequences affiliated with the haloalkaliphilic Natronomonas pharaonis .