Bacteria are central to the cycling of carbon (C), nitrogen (N) and phosphorus (P) in every ecosystem, yet our understanding of how tightly these cycles are coupled to bacterial biomass composition ...is based upon data from only a few species. Bacteria are commonly assumed to have high P content, low biomass C:P and N:P ratios, and inflexible stoichiometry. Here, we show that bacterial assemblages from lakes exhibit unprecedented flexibility in their P content (3% to less than 0.01% of dry mass) and stoichiometry (C:N:P of 28: 7: 1 to more than 8500: 1200: 1). The flexibility in C:P and N:P stoichiometry was greater than any species or assemblage, including terrestrial and aquatic autotrophs, and suggests a highly dynamic role for bacteria in coupling multiple element cycles.
Bacterial community structure (BCS) in freshwater ecosystems varies seasonally and due to physicochemical gradients, but metacommunity structure of a major river remains understudied. Here we ...characterize the BCS along the Mississippi River and contributing rivers in Minnesota over three years using Illumina next-generation sequencing, to determine how changes in environmental conditions as well as inputs from surrounding land and confluences impacted community structure. Contributions of sediment to water microbial diversity were also evaluated. Long-term variation in community membership was observed, and significant shifts in relative abundances of major freshwater taxa, including α-Proteobacteria, Burkholderiales, and Actinomycetales, were observed due to temporal and spatial variations. Environmental parameters (e.g. temperature, rainfall, and nutrient concentrations) primarily contributed to differences in phyla abundances (88% of variance), with minimal influence from spatial distance alone (<1% of variance). Furthermore, an annually-recurrent BCS was observed in late summer, further suggesting that seasonal dynamics strongly influence community composition. Sediment communities differed from those in the water, but contributed up to 50% to community composition in the water column. Among water sampling sites, 34% showed significant variability in BCS of replicate samples indicating variability among riverine communities due to heterogeneity in the water column. Results of this study highlight the need for a better understanding of spatial and temporal variations in riverine bacterial diversity associated with physicochemical gradients and reveal how communities in sediments, and potentially other environmental reservoirs, impact waterborne BCS. Techniques used in this study may prove useful to determine sources of microbes from sediments and soils to waterways, which will facilitate best management practices and total maximum daily load determinations.
•Upper Mississippi River bacterial communities were characterized over three years.•Community structure was correlated with changes in physicochemical parameters.•A reproducible community structure was observed in the late summer.•Species sorting and seasonal dynamics primarily drove shifts in community structure.•Sediment communities may also contribute significantly to planktonic communities.
For any enzyme-catalyzed reaction to occur, the corresponding protein-encoding genes and transcripts are necessary prerequisites. Thus, a positive relationship between the abundance of gene or ...transcripts and corresponding process rates is often assumed. To test this assumption, we conducted a meta-analysis of the relationships between gene and/or transcript abundances and corresponding process rates. We identified 415 studies that quantified the abundance of genes or transcripts for enzymes involved in carbon or nitrogen cycling. However, in only 59 of these manuscripts did the authors report both gene or transcript abundance and rates of the appropriate process. We found that within studies there was a significant but weak positive relationship between gene abundance and the corresponding process. Correlations were not strengthened by accounting for habitat type, differences among genes or reaction products versus reactants, suggesting that other ecological and methodological factors may affect the strength of this relationship. Our findings highlight the need for fundamental research on the factors that control transcription, translation and enzyme function in natural systems to better link genomic and transcriptomic data to ecosystem processes.
Display omitted
•The influence of ten biochars on rice grown on contaminated soil was investigated.•Biochars modified the composition of dissolved organic matter in soil solution.•DOM ...directly/indirectly controlled element mobility and element bioaccumulation.•High temperature biochars significantly (P ≤ 0.05) suppressed As/Cd uptake in rice.•AsIII (by all biochars), DMA and AsV (by SSBC350) uptake markedly decreased in rice.
Biochar application has attracted great attention due to its diverse uses and benefits in the fields of environmental management and agriculture. Biochar modifies the composition of dissolved organic matter (DOM) in soil, which directly or indirectly controls the mobility of metal contaminants and their bioaccumulation. In this study, ten different hydrothermal biochars pyrolysed from mushroom waste (MSBC), soybean straw (SBBC), sewage sludge (SSBC), peanut shells (PNBC) and rice straw (RSBC) at two pyrolysis temperatures (200 °C and 350 °C) were used to investigate DOM changes in soil solution and their effects on metal availability and bioaccumulation. Biochar induced modification of soil DOM which was characterized by spectroscopic analysis of water soluble organic carbon, specific absorbance (SUVA254), UV–vis absorption, spectral slope (SR) and the absorption coefficient. Regarding rice plant growth, the biochar effects on biomass were greatly varied. Biochars (except for RSBC and MSBC) prepared at high temperature significantly (P ≤ 0.05) suppressed the availability of As and Cd in soil and their subsequent bioaccumulation in rice plants. The highest reduction (88%) in bioaccumulated As was observed in rice grown on soil amended with SBBC prepared at 350 °C (the highest temperature for hydrothermal technique). The addition of biochars (except RSBC and MSBC) prepared at high temperature markedly (p < 0.05) decreased AsIII (30–92%), while the effects on dimethylarsenic acid (DMA) and arsenate (AsV) concentrations were not significant except for SSBC350 (prepared at 350 °C) treatment. These results highlight the potential of biochar-DOM interactions as an important mechanism for suppressing the mobility and bioaccumulation of As and Cd in biochar-amended paddy agricultural systems.
We explore the role of lakes in carbon cycling and global climate, examine the mechanisms influencing carbon pools and transformations in lakes, and discuss how the metabolism of carbon in the inland ...waters is likely to change in response to climate. Furthermore, we project changes as global climate change in the abundance and spatial distribution of lakes in the biosphere, and we revise the estimate for the global extent of carbon transformation in inland waters. This synthesis demonstrates that the global annual emissions of carbon dioxide from inland waters to the atmosphere are similar in magnitude to the carbon dioxide uptake by the oceans and that the global burial of organic carbon in inland water sediments exceeds organic carbon sequestration on the ocean floor. The role of inland waters in global carbon cycling and climate forcing may be changed by human activities, including construction of impoundments, which accumulate large amounts of carbon in sediments and emit large amounts of methane to the atmosphere. Methane emissions are also expected from lakes on melting permafrost. The synthesis presented here indicates that (1) inland waters constitute a significant component of the global carbon cycle, (2) their contribution to this cycle has significantly changed as a result of human activities, and (3) they will continue to change in response to future climate change causing decreased as well as increased abundance of lakes as well as increases in the number of aquatic impoundments.
The “freshwater pipe” concept has improved our understanding of freshwater carbon (C) cycling, however, it has rarely been applied to macronutrients such as nitrogen (N) or phosphorus (P). Here, we ...synthesize knowledge of the processing of C, N, and P together in freshwaters from land to the ocean. We compared flux estimates into and out of the N and P “pipes” and showed the net removal rates of N and P by inland waters were less than those for C. The C : N : P stoichiometry of inland water inputs vs. exports differed due to large respiratory C and N losses, and efficient P burial in inland waters. Residence time plays a critical role in the processing of these elements through the pipe, where higher water residence times from streams to lakes results in substantial increases in C : N, C : P, and N : P ratios.
The effects of resource stoichiometry and growth rate on the elemental composition of biomass have been examined in a wide variety of organisms, but the interaction among these effects is often ...overlooked. To determine how growth rate and resource imbalance affect bacterial carbon (C): nitrogen (N): phosphorus (P) stoichiometry and elemental content, we cultured two strains of aquatic heterotrophic bacteria in chemostats at a range of dilution rates and P supply levels (C:P of 100:1 to 10,000:1). When growing below 50% of their maximum growth rate, P availability and dilution rate had strong interactive effects on biomass C:N:P, elemental quotas, cell size, respiration rate, and growth efficiency. In contrast, at faster growth rates, biomass stoichiometry was strongly homeostatic in both strains (C:N:P of 70:13:1 and 73:14:1) and elemental quotas of C, N, and P were tightly coupled (but not constant). Respiration and cell size increased with both growth rate and P limitation, and P limitation induced C accumulation and excess respiration. These results show that bacterial biomass stoichiometry is relatively constrained when all resources are abundant and growth rates are high, but at low growth rates resource imbalance is relatively more important than growth rate in controlling bacterial biomass composition.
Taxonomic characterization of environmental microbial communities via high-throughput DNA sequencing has revealed that patterns in microbial biogeography affect community structure. However, shifts ...in functional diversity related to variation in taxonomic composition are poorly understood. To overcome limitations due to the prohibitive cost of high-depth metagenomic sequencing, tools to infer functional diversity based on phylogenetic distributions of functional traits have been developed. In this study we characterized functional microbial diversity at 11 sites along the Mississippi River in Minnesota using both metagenomic sequencing and functional-inference-based (PICRUSt) approaches. This allowed us to determine how distance and variation in land cover throughout the river influenced the distribution of functional traits, as well as to validate PICRUSt inferences. The distribution and abundance of functional traits, by metagenomic analysis, were similar among sites, with a median standard deviation of 0.0002% among tier 3 functions in KEGG. Overall inferred functional variation was significantly different (P ≤ 0.035) between two water basins surrounded by agricultural vs. developed land cover, and abundances of bacterial orders that correlated with functional traits by metagenomic analysis were greater where abundances of the trait were inferred to be higher. PICRUSt inferences were significantly correlated (r = 0.147, P = 1.80 × 10(-30)) with metagenomic annotations. Discrepancies between metagenomic and PICRUSt taxonomic-functional relationships, however, suggested potential functional redundancy among abundant and rare taxa that impeded the ability to accurately assess unique functional traits among rare taxa at this sequencing depth. Results of this study suggest that a suite of "core functional traits" is conserved throughout the river and distributions of functional traits, rather than specific taxa, may shift in response to environmental heterogeneity.
PDF
