Expression of the alpha 1-proteinase inhibitor gene family during evolution of the genus Mus

alpha 1-Proteinase inhibitors (alpha 1-PIs) are members of the serpin superfamily of proteinase inhibitors, and are important in the maintenance of homeostasis in a wide variety of animal taxa. Previous studies have shown that in mice (genus Mus), evolution of alpha 1-PIs is characterized by gene amplification, region-specific concerted evolution, and rapid accumulation of amino acid substitutions. The latter occurs primarily in the reactive center, which is the region of the alpha 1-PI molecule that determines the inhibitor's specificity for target proteinases. The P1 residue within the reactive center, which is methionine in so-called orthodox alpha 1-PIs and an amino acid other than methionine in unorthodox alpha 1-PIs, is a primary determinant of inhibitor specificity. In the present study, we find that the expression of mRNAs encoding unorthodox alpha 1-PIs is polymorphic within Mus species, i.e., among individuals or inbred strains. This is in striking contrast to mRNAs that encode orthodox alpha 1-PIs, whose concentrations are relatively invariant. The intraspecies variations in mRNA expression represent polymorphisms in the structure of the alpha 1- PI gene family. The results, taken together with previously described aspects of alpha 1-PI evolution, indicate that the dissimilar levels of polymorphism exhibited by orthodox and unorthodox alpha 1-PIs, which likely have distinct physiological functions, may reflect different levels of selective constraint. The significance of this finding to the evolution of gene families is discussed.      

Ecoenzymatic Stoichiometry in Relation to Productivity for Freshwater Biofilm and Plankton Communities

The degradation of detrital organic matter and assimilation of carbon (C), nitrogen (N), and phosphorus (P) by heterotrophic microbial communities is mediated by enzymes released into the environment (ecoenzymes). For the attached microbial communities of soils and freshwater sediments, the activities of β-glucosidase, β-N-acetylglucosaminidase, leucine aminopeptidase, and phosphatase show consistent stoichiometric patterns. To determine whether similar constraints apply to planktonic communities, we assembled data from nine studies that include measurements of these enzyme activities along with microbial productivity. By normalizing enzyme activity to productivity, we directly compared the ecoenzymatic stoichiometry of aquatic biofilm and bacterioplankton communities. The relationships between β-glucosidase and α-glucosidase and β-glucosidase and β-N-acetylglucosaminidase were statistically indistinguishable for the two community types, while the relationships between β-glucosidase and phosphatase and β-glucosidase and leucine aminopeptidase significantly differed. For β-glucosidase vs. phosphatase, the differences in slope (biofilm 0.65, plankton 1.05) corresponded with differences in the mean elemental C:P ratio of microbial biomass (60 and 106, respectively). For β-glucosidase vs. leucine aminopeptidase, differences in slope (0.80 and 1.02) did not correspond to differences in the mean elemental C:N of biomass (8.6 and 6.6). β-N-Acetylglucosaminidase activity in biofilms was significantly greater than that of plankton, suggesting that aminosaccharides were a relatively more important N source for biofilms, perhaps because fungi are more abundant. The slopes of β-glucosidase vs. (β-N-acetylglucosaminidase + leucine aminopeptidase) regressions (biofilm 1.07, plankton 0.94) corresponded more closely to the estimated difference in mean biomass C:N. Despite major differences in physical structure and trophic organization, biofilm and plankton communities have similar ecoenzymatic stoichiometry in relation to productivity and biomass composition. These relationships can be integrated into the stoichiometric and metabolic theories of ecology and used to analyze community metabolism in relation to resource constraints.     

Microbial Community Responses to Atmospheric Carbon Dioxide Enrichment in a Warm-Temperate Forest

Forest productivity depends on nutrient supply, and sustained increases in forest productivity under elevated carbon dioxide (CO₂) may ultimately depend on the response of microbial communities to changes in the quantity and chemistry of plant-derived substrates, We investigated microbial responses to elevated CO₂ in a warm-temperate forest under free-air CO₂ enrichment for 5 years (1997–2001). The experiment was conducted on three 30 m diameter plots under ambient CO₂ and three plots under elevated CO₂ (200 ppm above ambient). To understand how microbial processes changed under elevated CO₂, we assayed the activity of nine extracellular enzymes responsible for the decomposition of labile and recalcitrant carbon (C) substrates and the release of nitrogen (N) and phosphorus (P) from soil organic matter. Enzyme activities were measured three times per year in a surface organic horizon and in the top 15 cm of mineral soil. Initially, we found significant increases in the decomposition of labile C substrates in the mineral soil horizon under elevated CO₂; this overall pattern was present but much weaker in the O horizon. Beginning in the 4th year of this study, enzyme activities in the O horizon declined under elevated CO₂, whereas they continued to be stimulated in the mineral soil horizon. By year 5, the degradation of recalcitrant C substrates in mineral soils was significantly higher under elevated CO₂. Although there was little direct effect of elevated CO₂ on the activity of N- and P-releasing enzymes, the activity of nutrient-releasing enzymes relative to those responsible for C metabolism suggest that nutrient limitation is increasingly regulating microbial activity in the O horizon. Our results show that the metabolism of microbial communities is significantly altered by the response of primary producers to elevated CO₂. We hypothesize that ecosystem responses to elevated CO₂ are shifting from primary production to decomposition as a result of increasing nutrient limitation.     

Large-Scale Variation in Subsurface Stream Biofilms: A Cross-Regional Comparison of Metabolic Function and Community Similarity

We examined bacterial metabolic activity and community similarity in shallow subsurface stream sediments distributed across three regions of the eastern United States to assess whether there were parallel changes in functional and structural attributes at this large scale. Bacterial growth, oxygen consumption, and a suite of extracellular enzyme activities were assayed to describe functional variability. Community similarity was assessed using randomly amplified polymorphic DNA (RAPD) patterns. There were significant differences in streamwater chemistry, metabolic activity, and bacterial growth among regions with, for instance, twofold higher bacterial production in streams near Baltimore, MD, compared to Hubbard Brook, NH. Five of eight extracellular enzymes showed significant differences among regions. Cluster analyses of individual streams by metabolic variables showed clear groups with significant differences in representation of sites from different regions among groups. Clustering of sites based on randomly amplified polymorphic DNA banding resulted in groups with generally less internal similarity although there were still differences in distribution of regional sites. There was a marginally significant (p = 0.09) association between patterns based on functional and structural variables. There were statistically significant but weak (r ² ∼ 30%) associations between landcover and measures of both structure and function. These patterns imply a large-scale organization of biofilm communities and this structure may be imposed by factor(s) such as landcover and covariates such as nutrient concentrations, which are known to also cause differences in macrobiota of stream ecosystems.     

Seasonal and interannual variation of bacterial production in lowland rivers of the Orinoco basin

1. We examined the influence of hydrologic seasonality on temporal variation of planktonic bacterial production (BP) in relatively undisturbed lowland rivers of the middle Orinoco basin, Venezuela. We sampled two clearwater and two blackwater rivers over 2 years for dissolved organic carbon (DOC), chlorophyll, phosphorus and bacterial abundance to determine their relationship to temporal variation in BP. 2. Dissolved organic carbon concentration was greater in blackwater (543–664 μm ) than in clearwater rivers (184–240 μm ), and was generally higher during periods of rising and high water compared with low water. Chlorophyll concentration peaked (3 μg L^?1) during the first year of study when discharge was lowest, particularly in blackwater rivers. Soluble reactive phosphorus (SRP) was very low in the study rivers (<3.8 μg L^?1) and concentration increased during low water. 3. Average BP was higher in clearwater (0.20–0.26 μg C L^?1 h^?1) than in blackwater rivers (0.14–0.17 μg C L^?1 h^?1), although mean bacterial abundance was similar among rivers (0.6–0.8 × 10⁶ cells mL^?1). 4. Periods of higher chlorophyll a concentration (low water) or flushing of terrestrial organic material (rising water) were accompanied by higher BP, while low BP was observed during the period of high water. 5. Interannual variation in BP was influenced by variations in discharge related to El Niño Southern Oscillation events. 6. Seasonal variation in BP in the study rivers and other tropical systems was relatively small compared with seasonal variation in temperate rivers and lakes. In addition to the low seasonal variation of temperature in the tropics, low overall human disturbance could result in less variation in the inputs of nutrients and carbon to the study rivers compared with more disturbed temperate systems.     

Diversity and distribution of soil fungal communities in a semiarid grassland

The fungal loop model of semiarid ecosystems integrates microtopographic structures and pulse dynamics with key microbial processes. However limited data exist about the composition and structure of fungal communities in these ecosystems. The goal of this study was to characterize diversity and structure of soil fungal communities in a semiarid grassland. The effect of long-term nitrogen fertilization on fungi also was evaluated. Samples of rhizosphere (soil surrounding plant roots) and biological soil crust (BSC) were collected in central New Mexico, USA. DNA was amplified from the samples with fungal specific primers. Twelve clone libraries were generated with a total of 307 (78 operational taxonomic units, OTUs) and 324 sequences (67 OTUs) for BSC and rhizosphere respectively. Approximately 40% of soil OTUs were considered novel (less than 97% identity when compared to other sequences in NCBI using BLAST). The dominant organisms were dark-septate (melanized fungi) ascomycetes belonging to Pleosporales. Effects of N enrichment on fungi were not evident at the community level; however the abundance of unique sequences, sampling intensity and temporal variations may be uncovering the effect of N in composition and diversity of fungal communities. The fungal communities of rhizosphere soil and BSC overlapped substantially in composition, with a Jaccard abundance similarity index of 0.75. Further analyses are required to explore possible functions of the dominant species colonizing zones of semiarid grassland soils.     

Effect of long-term nitrogen fertilization on mycorrhizal fungi associated with a dominant grass in a semiarid grassland

We studied the diversity of arbuscular mycorrhizal fungi (AMF) in semiarid grassland and the effect of long-term nitrogen (N) fertilization on this fungal community. Root samples of Bouteloua gracilis were collected at the Sevilleta National Wildlife Refuge (New Mexico, USA) from control and N-amended plots that have been fertilized since 1995. Small subunit rDNA was amplified using AMF specific primers NS31 and AM1. The diversity of AMF was low in comparison with other ecosystems, only seven operational taxonomic units (OTU) were found in B. gracilis and all belong to the genus Glomus. The dominant OTU was closely related to the ubiquitous G. intraradices/G. fasciculatum group. N-amended plots showed a reduction in the abundance of the dominant OTU and an increase in AMF diversity. The greater AMF diversity in roots from N-amended plots may have been the result of displacement of the dominant OTU, which facilitated detection of uncommon AMF. The long-term implications of AMF responses to N enrichment for plant carbon allocation and plant community structure remain unclear.     

Soil carbon loss with warming: New evidence from carbon‐degrading enzymes

Climate warming affects soil carbon (C) dynamics, with possible serious consequences for soil C stocks and atmospheric CO₂ concentrations. However, the mechanisms underlying changes in soil C storage are not well understood, hampering long‐term predictions of climate C‐feedbacks. The activity of the extracellular enzymes ligninase and cellulase can be used to track changes in the predominant C sources of soil microbes and can thus provide mechanistic insights into soil C loss pathways. Here we show, using meta‐analysis, that reductions in soil C stocks with warming are associated with increased ratios of ligninase to cellulase activity. Furthermore, whereas long‐term (≥5 years) warming reduced the soil recalcitrant C pool by 14%, short‐term warming had no significant effect. Together, these results suggest that warming stimulates microbial utilization of recalcitrant C pools, possibly exacerbating long‐term climate‐C feedbacks.     

Ecoenzymatic stoichiometry of recalcitrant organic matter decomposition: the growth rate hypothesis in reverse

The flow of carbon and nutrients from plant production into detrital food webs is mediated by microbial enzymes released into the environment (ecoenzymes). Ecoenzymatic activities are linked to both microbial metabolism and environmental resource availability. In this paper, we extend the theoretical and empirical framework for ecoenzymatic stoichiometry from nutrient availability to carbon composition by relating ratios of ??-1,4-glucosidase (BG), acid (alkaline) phosphatase (AP), ??-N-acetylglucosaminidase (NAG), leucine aminopeptidase (LAP) and phenol oxidase (POX) activities in soils to measures of organic matter recalcitrance, using data from 28 ecosystems. BG and POX activities are uncorrelated even though both are required for lignocellulose degradation. However, the ratio of BG:POX activity is negatively correlated with the relative abundance of recalcitrant carbon. Unlike BG, POX activity is positively correlated with (NAG + LAP) and AP activities. We propose that the effect of organic matter recalcitrance on microbial C:N and C:P threshold element ratios (TER) can be represented by normalizing BG, AP and (NAG + LAP) activities to POX activity. The scaling relationships among these ratios indicate that the increasing recalcitrance of decomposing organic matter effectively reverses the growth rate hypothesis of stoichiometric theory by decreasing carbon and nutrient availability and slowing growth, which increases TER_N:P. This effect is consistent with the narrow difference between the mean elemental C:N ratios of soil organic matter and microbial biomass and with the inhibitory effect of N enrichment on rates of decomposition and microbial metabolism for recalcitrant organic matter. From these findings, we propose a conceptual framework for bottom-up decomposition models that integrate the stoichiometry of ecoenzymatic activities into general theories of ecology.