Prediction of the Metabolic Activity of a Mixed Bacillus Culture during the Biodegradation of Wastewater from the Potato Industry

The advantages of the analysis of electrical impedance changes for the prediction of the metabolic activity of mixed Bacillus cultures used for high temperature industrial wastewater utilization are demonstrated. The primary aim of this study was to investigate the possibilities of a fast assessment of the biodegradative capabilities of microorganisms, their requirements regarding the medium composition as well as the inhibiting effect of high‐strength (i.e., highly concentrated) wastewaters on microbial growth. Four mixed Bacillus cultures were cultivated at 45 and 55 °C on two kinds of wastewater from the potato starch industry. The course of changes in the electrical impedance during the cultivation of the bacteria in the examined wastewaters was described by the mathematical Gompertz model. Three kinetics parameters (maximum rate of impedance changes, I_max; the time necessary to reach, I_max, T_I; and the duration of the lag phase, λ) were proposed for the statistical analysis of the bacterial metabolic activity. The temperature of the biodegradation process and the type and strength of the wastewater significantly influenced the microbial metabolic activity of the mixed bacterial cultures used. Monitoring of the impedance changes, caused by microbial metabolism, and its proposed mathematical specification allowed for predicting the dynamics of the microbiological degradation of wastewater and estimating the inhibiting effects of these media on the microorganisms.     

Long-term effect of re-vegetation on the microbial community of a severely eroded soil in sub-tropical China

The long-term (18 years) effects of re-vegetating eroded soil on soil microbial biomass, community structure and diversity were investigated in a forest soil derived from Quaternary clay in the Red Soil Ecological Experimental Station of the Chinese Academy of Sciences. Large areas of land in this region of China have been subjected to severe soil erosion, characterised by the removal of the fertile surface soil and even the exposure of parental rock in some areas due to a combination of deforestation and heavy rainfall. The effects of planting eroded or uneroded soil with Pinus massoniana, Cinnamomum camphora or Lespedeza bicolor on the soil microbial community and chemical properties were assessed. Total soil microbial community DNA was extracted and bacterial 16 S rRNA gene fragments were amplified by PCR and analysed by terminal restriction fragment length polymorphism (T-RFLP). Microbial biomass carbon (C_mic) was measured by chloroform fumigation-extraction. Following the restoration there were significant increases in both C_mic and bacterial diversity (Shannon index), and significant changes in bacterial community structure. Erosion factors were significant only in minor dimensions suggesting that the restoration had been largely successful in terms of bacterial community structure. Compared with uneroded soil, C_mic recovered in L. bicolor and P. massoniana restored eroded plots and was significantly greater under these tree species than C. camphora, although soils in C. camphora restored plots displayed the highest bacterial diversity. The recovery of microbial biomass and diversity in the eroded plots was, to large extent, accompanied by the development of the same bacterial community structure as in the uneroded plots with erosion having relatively little effect on bacterial community structure.     

Formation of biomass,total protein,chlorophylls, lipids and fatty acids in green and blue-green algae during one growth phase.

Batch cultures (8–32 l.) of Chlorella vulgaris and Scenedesmus obliquus and of Anacystis nidulans and Microcystis aeruginosa were grown in media containing 0.001 % KNO₃ and at several stages in growth sampled for biomass, total protein, chlorophylls, lipids and fatty acids. With increasing time and decreasing nitrogen concentrations, the biomass of all of the algae increased, whereas the total protein and chlorophyll content dropped. Green and blue-green algae, however, behaved differently in their lipid metabolism. In the green algae the total lipid and fatty acid content as well as the composition of these compounds changed considerably during one growth phase and was dependent on the nitrogen concentration in the media at any given day of growth. More specifically, during the initial stages of growth the green algae produced larger amounts of polar lipids and polyunsaturated C₁₆ and C₁₈ fatty acids. Towards the end of growth, however, these patterns changed in that the main lipids of the green algae were neutral with mainly saturated fatty acids (mostly 18:1 and 16:0). Such changes did not occur in the blue-green algae. These differences between prokaryotic and eukaryotic algae can possibly be explained by the ‘endosymbiont theory’.     

Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

The impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected, Burkholderiales and Rhodocyclales of the Betaproteobacteria class were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.     

Monitoring the microbial community succession and diversity of Liangzhou fumigated vinegar during solid-state fermentation with next-generation sequencing

This study reveals the microbial community succession and diversity during the whole solid-fermentation processes of naturally fermented Liangzhou fumigated vinegar (LZFV). Dynamics and diversity of microbial community succession in “Daqu” starter and other fermentation stages (starch saccharification, alcoholic fermentation, and acetic acid fermentation) were monitored using a metagenomic approach involving high-throughput sequencing. Meanwhile, dynamic changes of characteristic flavor compounds of vinegar were determined by gas chromatograph (GC) analysis. The result showed that the microbiota composition exhibited rich diversity. Twenty-five bacterial and 18 fungal genera were found in the whole fermentation process where Lactobacillus, Acetobacter, Aspergillus, Saccharomyces, and Alternaria were the predominant microorganisms. Alpha diversity metrics showed that bacterial diversity in Daqu was greater than that in AF and AAF. By contrast, fungal diversity increased from Daqu to AF and decreased in the initial stage (5–8 days) of AAF then remained relatively steady. Hence, these results could help understand dynamics of microbial community succession in continuous fermentation of traditional Chinese vinegars. The LZFV fermentation is a continuous process with spontaneous growth that affects the dynamics of microbial communities. Continuous changes of micro-environment conditions in substrate affect the diversity and structure of microbiota. Microbial growth and metabolism were closely related to the changes in the physicochemical characteristics of the cultures. The microbial flora composition showed rich diversity, and with the increase in brewing time and the change in micro-ecological environmental conditions; the microbial community showed a complex dynamic changes.

     

Understanding how lake populations of arctic char are structured and function with special consideration of the potential effects of climate change: a multi-faceted approach

Size dimorphism in fish populations, both its causes and consequences, has been an area of considerable focus; however, uncertainty remains whether size dimorphism is dynamic or stabilizing and about the role of exogenous factors. Here, we explored patterns among empirical vital rates, population structure, abundance and trend, and predicted the effects of climate change on populations of arctic char (Salvelinus alpinus) in two lakes. Both populations cycle dramatically between dominance by small (≤300 mm) and large (>300 mm) char. Apparent survival (Φ) and specific growth rates (SGR) were relatively high (40–96 %; SGR range 0.03–1.5 %) and comparable to those of conspecifics at lower latitudes. Climate change scenarios mimicked observed patterns of warming and resulted in temperatures closer to optimal for char growth (15.15 °C) and a longer growing season. An increase in consumption rates (28–34 %) under climate change scenarios led to much greater growth rates (23–34 %). Higher growth rates predicted under climate change resulted in an even greater predicted amplitude of cycles in population structure as well as an increase in reproductive output (R _o) and decrease in generation time (G _o). Collectively, these results indicate arctic char populations (not just individuals) are extremely sensitive to small changes in the number of ice-free days. We hypothesize years with a longer growing season, predicted to occur more often under climate change, produce elevated growth rates of small char and act in a manner similar to a “resource pulse,” allowing a sub-set of small char to “break through,” thus setting the cycle in population structure.     

A Regulatory Mutant of Hansenula polymorpha Exhibiting Methanol Utilization Metabolism and Peroxisome Proliferation in Glucose

Mutant LGM-128 of Hansenula polymorpha harbors the recessive mutation glr2-1 which confers a complex pleiotropic phenotype, the major feature of which is the metabolically unnecessary induction of methanol utilization metabolism (C₁ metabolism) during growth on glucose, whether or not methanol is in the medium. Therefore, in this mutant, peroxisomes are formed and proliferate upon cultivation in glucose-containing media. In these media, LGM-128 shows induction levels of C₁ metabolism that are similar to those observed in methanol-containing media. This indicates that GLR2 controls the repression-derepression process stimulated by glucose and that the induction process triggered by methanol plays only a minor role in activating C₁ metabolism. Cultivating LGM-128 in methanol and then transferring it to glucose media revealed that active degradative processes occur, leading to the disappearance of C₁ metabolism. This observation suggests that, although stimulated by glucose, the two processes are controlled by elements which are, at least in part, distinct. Finally, glr2-1 does not affect ethanol repression, suggesting that in H. polymorpha the two repressing circuits are separated.     

Characterization of halotolerant and oligotrophic bacterial communities in Asian desert dust (KOSA) bioaerosol accumulated in layers of snow on Mount Tateyama, Central Japan

Microbial particles transported by Asian desert dust (KOSA) possibly impact ecosystems and human health in downwind environments and are commonly called ??bioaerosols.?? The microbial communities associated with KOSA mineral particles (KOSA bioaerosol), which were collected from the snow cover on Mt. Tateyama, were investigated by means of a culture-amendment technique combined with denaturing gradient gel electrophoresis (DGGE) analysis using 16S rRNA genes. After the stratigraphy of the snow layer formed on the walls of a snow pit on Mt. Tateyama, samples were collected from 2 layers, which included KOSA particles and one which did not. The snow samples with KOSA particles indicated microbial growth in the 10⁰ and 10^?1 dilution media and in the medium with NaCl below 10%, while the snow sample without KOSA particles showed no microbial growth in the culture media. The PCR?CDGGE analysis revealed that the bacterial compositions in the snow samples including KOSA mineral particles were mainly composed of the members of the phyla Actinobacteria, Firmicutus, and Proteobacteria. In particular, the 2 phylotypes appeared in the microbial cultures were similar to the members of the B. subtilis group, which has been detected in bioaerosol samples collected from the atmosphere over KOSA arrival (Suzu City) and source (Dunhuang City) regions. Presumably, halotolerant and oligotrophic bacterial communities are associated with the KOSA particles that descend to the snow cover on Mt. Tateyama.     

Diversity,Distribution and Hydrocarbon Biodegradation Capabilities of Microbial Communities in Oil-Contaminated Cyanobacterial Mats from a Constructed Wetland

Various types of cyanobacterial mats were predominant in a wetland, constructed for the remediation of oil-polluted residual waters from an oil field in the desert of the south-eastern Arabian Peninsula, although such mats were rarely found in other wetland systems. There is scarce information on the bacterial diversity, spatial distribution and oil-biodegradation capabilities of freshwater wetland oil-polluted mats. Microbial community analysis by Automated Ribosomal Spacer Analysis (ARISA) showed that the different mats hosted distinct microbial communities. Average numbers of operational taxonomic units (OTUs_ARISA) were relatively lower in the mats with higher oil levels and the number of shared OTUs_ARISA between the mats was <60% in most cases. Multivariate analyses of fingerprinting profiles indicated that the bacterial communities in the wetland mats were influenced by oil and ammonia levels, but to a lesser extent by plant density. In addition to oil and ammonia, redundancy analysis (RDA) showed also a significant contribution of temperature, dissolved oxygen and sulfate concentration to the variations of the mats’ microbial communities. Pyrosequencing yielded 282,706 reads with >90% of the sequences affiliated to Proteobacteria (41% of total sequences), Cyanobacteria (31%), Bacteriodetes (11.5%), Planctomycetes (7%) and Chloroflexi (3%). Known autotrophic (e.g. Rivularia) and heterotrophic (e.g. Azospira) nitrogen-fixing bacteria as well as purple sulfur and non-sulfur bacteria were frequently encountered in all mats. On the other hand, sequences of known sulfate-reducing bacteria (SRBs) were rarely found, indicating that SRBs in the wetland mats probably belong to yet-undescribed novel species. The wetland mats were able to degrade 53–100% of C₁₂–C₃₀ alkanes after 6 weeks of incubation under aerobic conditions. We conclude that oil and ammonia concentrations are the major key players in determining the spatial distribution of the wetland mats’ microbial communities and that these mats contribute directly to the removal of hydrocarbons from oil field wastewaters.     

The influence of casein and urea as nitrogen sources on in vitro equine caecal fermentation

To access the fermentative response of equine caecal microbial population to nitrogen availability, an in vitro study was conducted using caecal contents provided with adequate energy sources and nitrogen as limiting nutrient. Two nitrogen (N) sources were provided, protein (casein) and non-protein (urea). Caecal fluid, taken from three cannulated horses receiving a hay–concentrate diet, was mixed with a N-free buffer–mineral solution. The influence of four N levels (3.7, 6.3, 12.5 or 25 mg of N in casein or urea) was studied using the gas production technique. Total volatile fatty acids (VFA), NH₃-N and gas production were measured after a 24-h incubation period. Microbial biomass was estimated using adenine and guanine bases as internal markers, and ATP production was estimated stoichiometrically. Microbial growth efficiency (Y_ATP) and gas efficiency (E_gas) were estimated. Fermentation with casein as the sole N source was generally characterized by lower total VFA, NH₃-N, total gas production and higher acetate : propionate (A : P) ratio and Y_ATP than with urea. Results herein presented indicate that, under these in vitro conditions, caecal microbial population does in fact use urea N, but less efficiently than casein in terms of microbial growth.     

Dormant state and phenotypic variability of Staphylococcus aureus and Corynebacterium pseudodiphtheriticum

Ability to produce dormant forms (DF) was demonstrated for non-spore-forming bacteria Staphylococcus aureus (a nonpathogenic strain) and Corynebacterium pseudodiphtheriticum (an organism of the normal oropharyngeal flora). The salient features of the sthaphylococcal and corynebacterial DF were (1) prolonged (4 months) preservation of viability; (2) resistance to damaging factors (heat treatment); and (3) specific morphology and ultrastructure. The optimal conditions for DF formation were (1) transfer of stationary-phase cultures into saline solution with CaCl₂ (10–300 mM) (for S. aureus); (2) growth in SR1 synthetic medium with fivefold nitrogen limitation (for C. pseudodiphtheriticum); and (3) incubation with (1–5) × 10^?4 M of C₁₂-AHB, an alkylhydroxybenzene akin to microbial anabiosis autoinducers. Increase of C₁₂-AHB concentration to 7 × 10^?4–2 × 10^?3 M resulted in “mummification” of cells with irreversible loss of viability without autolytic processes. Germination of dormant forms was followed by increasing of phenotypic variability, as seen from (1) diversity of colony types and (2) emergence of antibiotic-resistant clones on selective media. The share of kanamycin-resistant S. aureus variants was most numerous (0.002–0.01%) in 4-month DF suspensions in SALINE with CaCl₂. In the C. pseudodiphtheriticum DF produced under the effect of C₁₂-AHB, the share of kanamycin-resistant variants was also found to increase. These data point to an association between the emergence of antibiotic-resistant variants of bacteria and their persistence in dormant state mediated by starvation stress and regulated by AHB.     

Elevated CO2 and nitrate levels increase wheat root-associated bacterial abundance and impact rhizosphere microbial community composition and function

Elevated CO₂ stimulates plant growth and affects quantity and composition of root exudates, followed by response of its microbiome. Three scenarios representing nitrate fertilization regimes: limited (30 ppm), moderate (70 ppm) and excess nitrate (100 ppm) were compared under ambient and elevated CO₂ (eCO₂, 850 ppm) to elucidate their combined effects on root-surface-associated bacterial community abundance, structure and function. Wheat root-surface-associated microbiome structure and function, as well as soil and plant properties, were highly influenced by interactions between CO₂ and nitrate levels. Relative abundance of total bacteria per plant increased at eCO₂ under excess nitrate. Elevated CO₂ significantly influenced the abundance of genes encoding enzymes, transporters and secretion systems. Proteobacteria, the largest taxonomic group in wheat roots (~ 75%), is the most influenced group by eCO₂ under all nitrate levels. Rhizobiales, Burkholderiales and Pseudomonadales are responsible for most of these functional changes. A correlation was observed among the five gene-groups whose abundance was significantly changed (secretion systems, particularly type VI secretion system, biofilm formation, pyruvate, fructose and mannose metabolism). These changes in bacterial abundance and gene functions may be the result of alteration in root exudation at eCO₂, leading to changes in bacteria colonization patterns and influencing their fitness and proliferation.Subject terms: Microbiome, Microbial ecology, Metagenomics, Microbial ecology     

Polyphasic characterization of four soil-derived phenanthrene-degrading Acidovorax strains and proposal of Acidovorax carolinensis sp. nov.

Four bacterial strains identified as members of the Acidovorax genus were isolated from two geographically distinct but similarly contaminated soils in North Carolina, USA, characterized, and their genomes sequenced. Their 16S rRNA genes were highly similar to those previously recovered during stable-isotope probing (SIP) of one of the soils with the polycyclic aromatic hydrocarbon (PAH) phenanthrene. Heterotrophic growth of all strains occurred with a number of organic acids, as well as phenanthrene, but no other tested PAHs. Optimal growth occurred aerobically under mesophilic temperature, neutral pH, and low salinity conditions. Predominant fatty acids were C_16:1ω7c/C_16:1ω6c, C_16:0, and C_18:1ω7c, and were consistent with the genus. Genomic G + C contents ranged from 63.6 to 64.2%. A combination of whole genome comparisons and physiological analyses indicated that these four strains likely represent a single species within the Acidovorax genus. Chromosomal genes for phenanthrene degradation to phthalate were nearly identical to highly conserved regions in phenanthrene-degrading Delftia, Burkholderia, Alcaligenes, and Massilia species in regions flanked by transposable or extrachromosomal elements. The lower degradation pathway for phenanthrene metabolism was inferred by comparisons to described genes and proteins. The novel species Acidovorax carolinensis sp. nov. is proposed, comprising the four strains described in this study with strain NA3^T as the type strain (=LMG 30136, =DSM 105008).     

Correlation of foliage and litter chemistry of sugar maple, Acer saccharum, as affected by elevated CO2 and varying N availability, and effects on decomposition

Rising atmospheric carbon dioxide has the potential to alter leaf litter chemistry, potentially affecting decomposition and rates of carbon and nitrogen cycling in forest ecosystems. This study was conducted to determine whether growth under elevated atmospheric CO₂ altered the quality and microbial decomposition of leaf litter of a widely distributed northern hardwood species at sites of low and high soil nitrogen availability. In addition, we assessed whether the carbon–nutrient balance (CNB) and growth differentiation balance (GDB) hypotheses could be extended to predict changes in litter quality in response to resource availability. Sugar maple (Acer saccharum) was grown in the field in open‐top chambers at 36 and 55 Pa partial pressure CO₂, and initial soil mineralization rates of 45 and 348 μg N g^?1 d^?1. Naturally senesced leaf litter was assessed for chemical composition and incubated in the laboratory for 111 d. Microbial respiration and the production of dissolved organic carbon (DOC) were quantified as estimates of decomposition. Elevated CO₂ and low soil nitrogen resulted in higher litter concentrations of nonstructural carbohydrates and condensed tannins, higher C/N ratios and lower N concentrations. Soil N availability appears to have had a greater effect on litter quality than did atmospheric CO₂, although the treatments were additive, with highest concentrations of nonstructural carbohydrates and condensed tannins occurring under elevated CO₂–low soil N. Rates of microbial respiration and the production of DOC were insensitive to differences in litter quality. In general, concentrations of litter constituents, except for starch, were highly correlated to those in live foliage, and the CNB/GDB hypotheses proved useful in predicting changes in litter quality. We conclude the chemical composition of sugar maple litter will change in the future in response to rising atmospheric CO₂, and that soil N availability will exert a major control. It appears that microbial metabolism will not be directly affected by changes in litter quality, although conclusions regarding decomposition as a whole must consider the entire soil food web.     

Effect of monospecific and mixed Cunninghamia lanceolata plantations on microbial community and two functional genes involved in nitrogen cycling

Conversion of native broadleaf forest (NF) and introduction of broadleaf species into monospecific Cunninghamia lanceolata plantations are silvicultural practices driven by the increasing demand for timber production. This study was conducted to evaluate the impacts of successive planting of C. lanceolata and mixed plantations (C. lanceolata-Michelia macclurei, CFM; C. lanceolata-Alnus cremastogyne, CFA; C. lanceolata-Kalopanax septemlobus, CFK) on microbial community diversity. Microbial biomass (MBC) was assessed using chloroform fumigation-extraction. Using denaturing gradient gel electrophoresis (DGGE), we examined the biodiversity within eubacterial (16S rRNA gene) and fungal (28S rRNA gene) species and two genes involved in N cycling: nifH and amoA. Microbial community diversities and microbial biomass decreased as NF was substituted by successive plantings of C. lanceolata plantations, whereas the trend reversed after introducing the broadleaf, M. macclurei, into pure C. lanceolata plantations. A strong positive correlation between MBC changes and total organic C (TOC), total organic N (TON), available N and extractable C (C_ext) were seen, which suggests that MBC was tightly coupled with the content of soil organic matter. The Shannon index showed that bacterial diversity and two functional genes (nifH and amoA) diversities associated with monospecific C. lanceolata plantations were lower than that of NF or mixed C. lanceolata plantations, such as CFM and CFA, whereas the opposite was seen for fungal diversity. Bacterial diversity was positively correlated with pH, TOC, TON, C_ext and NH ₄ ⁺ -N; while fungal diversity was positively correlated with C/N ratio and negatively correlated with pH. Both nitrogen fixing and ammonia oxidizing bacterial diversities were positively correlated with pH. Thus, soil pH was not only significantly positively correlated with bacterial diversity (r?=?0.502, P?<?0.05), nifH gene diversity (r?=?0.564, P?<?0.01) and amoA gene diversity (r?=?0.659, P?<?0.001), but also negatively correlated with fungal diversity (r?=?? 0.505, P?<?0.05), which seemed to be responsible for the discrimination of the soil microbial communities among these plantations. These findings suggest that different silvicultural practices have significant impacts on the soil microbial community through influences on soil chemical properties.     

Mutations That Extend the Specificity of the Endonuclease Activity of λ Terminase

Terminase, an enzyme encoded by the Nu1 and A genes of bacteriophage lambda, is crucial for packaging concatemeric DNA into virions. cosN, a 22-bp segment, is the site on the virus chromosome where terminase introduces staggered nicks to cut the concatemer to generate unit-length virion chromosomes. Although cosN is rotationally symmetric, mutations in cosN have asymmetric effects. The cosN G₂C mutation (a G-to-C change at position 2) in the left half of cosN reduces the phage yield 10-fold, whereas the symmetric mutation cosN C₁₁G, in the right half of cosN, does not affect the burst size. The reduction in phage yield caused by cosN G₂C is correlated with a defect in cos cleavage. Three suppressors of the cosN G₂C mutation, A-E₅₁₅G, A-N₅₀₉K, and A-R₅₀₄C, have been isolated that restore the yield of λ cosN G₂C to the wild-type level. The suppressors are missense mutations that alter amino acids located near an ATPase domain of gpA. λ A-E₅₁₅G, A-N₅₀₉K, and A-R₅₀₄C phages, which are cosN⁺, also had wild-type burst sizes. In vitro cos cleavage experiments on cosN G₂C C₁₁G DNA showed that the rate of cleavage for A-E₅₁₅G terminase is three- to fourfold higher than for wild-type terminase. The A-E₅₁₅G mutation changes residue 515 of gpA from glutamic acid to glycine. Uncharged polar and hydrophobic residues at position 515 suppressed the growth defect of λ cosN G₂C C₁₁G. In contrast, basic (K, R) and acidic (E, D) residues at position 515 failed to suppress the growth defect of λ cosN G₂C C₁₁G. In a λ cosN⁺ background, all amino acids tested at position 515 were functional. These results suggest that A-E₅₁₅G plays an indirect role in extending the specificity of the endonuclease activity of λ terminase.     

Land cover change effects on soil chemical and biological properties after planting Mongolian pine (Pinus sylvestris var. mongolica) in sandy lands in Keerqin, northeastern China

We compared soil moisture content, pH, total organic carbon (C _org), total nitrogen (TN), total phosphorus (TP) and inorganic N (NH₄ ⁺–N, NO₃ ^?–N) concentrations, soil potential C and N mineralization rates, soil microbial biomass C (C _mic), soil metabolic quotient (qCO₂), soil microbial quotient (C _mic/C _org) and soil enzyme (urease and invertase) activities in semiarid sandy soils under three types of land cover: grassland, Mongolian pine (Pinus sylvestris var. mongolica) plantation, and elm (Ulmus punila)–grass savanna in southeastern Keerqin, in northeast China. Soil C _org, TN and TP concentrations (0–10, 10–20, 20–40 and 40–60 cm) were lower while soil C/N and C/P ratios were higher in the plantation than in grassland and savanna. The effects of land cover change on NH₄ ⁺–N and NO₃ ^?–N concentrations, soil potential nitrification and C mineralization rates in the surface soil (0–10 cm) were dependent on sampling season; but soil potential N mineralization rates were not affected by land cover type and sampling season. The effects of land cover change on C _mic and qCO₂ of surface soil were not significant; but C _mic/C _org were significantly affected by land cover change and sampling season. We also found that land cover change, sampling season and land cover type?×?sampling season interaction significantly influenced soil enzyme (urease and invertase) activities. Usually soil enzyme activities were lower in the pine plantations than in grassland and savanna. Our results suggest that land cover change markedly influenced soil chemical and biological properties in sandy soils in the semiarid region, and these effects vary with sampling season.     

Activity-based cell sorting reveals responses of uncultured archaea and bacteria to substrate amendment

Metagenomic studies have revolutionized our understanding of the metabolic potential of uncultured microorganisms in various ecosystems. However, many of these genomic predictions have yet to be experimentally tested, and the functional expression of genomic potential often remains unaddressed. In order to obtain a more thorough understanding of cell physiology, novel techniques capable of testing microbial metabolism under close to in situ conditions must be developed. Here, we provide a benchmark study to demonstrate that bioorthogonal non-canonical amino acid tagging (BONCAT) in combination with fluorescence-activated cell sorting (FACS) and 16S rRNA gene sequencing can be used to identify anabolically active members of a microbial community incubated in the presence of various growth substrates or under changing physicochemical conditions. We applied this approach to a hot spring sediment microbiome from Yellowstone National Park (Wyoming, USA) and identified several microbes that changed their activity levels in response to substrate addition, including uncultured members of the phyla Thaumarchaeota, Acidobacteria, and Fervidibacteria. Because shifts in activity in response to substrate amendment or headspace changes are indicative of microbial preferences for particular growth conditions, results from this and future BONCAT-FACS studies could inform the development of cultivation media to specifically enrich uncultured microbes. Most importantly, BONCAT-FACS is capable of providing information on the physiology of uncultured organisms at as close to in situ conditions as experimentally possible.Subject terms: Environmental microbiology, Microbial communities, Microbial ecology, Archaea     

TheDPL1Gene Is Involved in Mediating the Response to Nutrient Deprivation inSaccharomyces cerevisiae

Sphingosine-1-phosphate is a sphingolipid metabolite involved in the regulation of cell proliferation in mammalian cells. The major route of sphingosine-1-phosphate degradation is through cleavage at the C_2–3bond by sphingosine phosphate lyase. The recent identification of the first dihydrosphingosine/sphingosine phosphate lyase gene inSaccharomyces cerevisiaeestablishes that phosphorylated sphingoid base metabolism is conserved throughout evolution. Thedpl1Δ deletion mutant, which accumulates endogenous phosphorylated sphingoid bases, exhibits unregulated proliferation upon approach to stationary phase. The increased proliferation rate during respiratory growth was associated with failure to appropriately recruit cells into the G₁phase of the cell cycle. Several genes were found to be overexpressed or prematurely expressed during nutrient deprivation in thedpl1Δ strain, including glucose-repressible genes and G₁cyclins. These studies implicate a role forDPL1and phosphorylated sphingoid bases in the regulation of global responses to nutrient deprivation in yeast.     

Early life-history processes in benthic octopus: Relationships between temperature, feeding, food conversion, and growth in juvenile Octopus pallidus

Initial growth in cephalopods is exponential, making early life-history critical in determining growth trajectories. Few captive studies have however examined the early life-history of cephalopods in fluctuating temperatures as would be encountered in the wild. This study investigates the relationship between early growth and the significant factors affecting growth, namely food intake, food conversion and fluctuating environmental temperatures. Pale octopus (Octopus pallidus) hatchlings were reared in captivity under either a warming or cooling temperature regime. Individual variations and periodicity in feeding rates (F_r), food conversion rates (C_r), growth rates (G_r), and the relationship between these variables and temperature were examined weekly. Food conversion rates were variable between individuals but also within individual octopus, which exhibited large fluctuations in C_r over time, exceeding 100% d^− 1 in one instance. Although individual F_r, C_r and G_r displayed fluctuations over time, there was no evidence of periodicity for any of the variables. Changes in temperature were not significantly correlated to changes in F_r, C_r or G_r. Feeding rate did not appear to influence growth rate or food conversion rate. Food conversion rate was negatively correlated to feeding rate in the same week, and positively correlated to growth rate. Short periods of low or no food consumption were common and the high values obtained for food conversion rate for some individuals suggest that octopus can grow substantially with little or no food intake. Individual variability observed in octopus growth may be dependent on the growth mechanism involved, specifically a fine balance between the continuous hyperplasic and hypertrophic growth found in cephalopods.