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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.

Ponds, wetlands, and shallow lakes (collectively “shallow waterbodies”) are among the most biogeochemically active freshwater ecosystems. Measurements of gross primary production (GPP), respiration (R), and net ecosystem production (NEP) are rare in shallow waterbodies compared to larger and deeper lakes, which can bias our understanding of lentic ecosystem processes. In this study, we calculated GPP, R, and NEP in 26 small, shallow waterbodies across temperate North America and Europe. We observed high rates of GPP (mean 8.4 g O2 m−3 d−1) and R (mean −9.1 g O2 m−3 d−1), while NEP varied from net heterotrophic to autotrophic. Metabolism rates were affected by depth and aquatic vegetation cover, and the shallowest waterbodies had the highest GPP, R, and the most variable NEP. The shallow waterbodies from this study had considerably higher metabolism rates compared to deeper lakes, stressing the importance of these systems as highly productive biogeochemical hotspots.

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.

Inland waters are important sources of the greenhouse gases carbon dioxide (CO2) and methane (CH4). Ponds have amongst the highest CO2 and CH4 fluxes of all aquatic ecosystems, yet seasonal variation in fluxes remain poorly characterized, creating challenges for accurately estimating annual emissions. Further, ponds can exhibit a range of mixing regimes, yet the impact of mixing regimes on gas emissions remains unclear. Here, we assessed annual dynamics of CO2 and CH4 in four temperate ponds (Minnesota, USA) that varied in mixing regimes. The ponds ranged from annual sinks to sources of CO2 (−1 to 15 mol m−2 yr−1) and were all significant sources of CH4 (4.3–8.2 mol m−2 yr−1), with annual fluxes in CO2 equivalents of 1.8–4.1 kg CO2-eq. m−2 yr−1. Mixing regimes impacted CO2 and CH4 dynamics, as stratified periods were associated with more anoxia, greater accumulation of gases in the bottom waters, higher emissions of CH4, and lower fluxes of CO2. Ponds with stronger summer stratification also had increased CO2 and CH4 fluxes associated with fall turnover. Overall, the two ponds with the strongest stratification had higher annual fluxes (2.6, 4.1 kg CO2-eq. m−2 yr−1) compared to the two ponds that more frequently mixed (1.8, 2.2 kg CO2-eq. m−2 yr−1).

SignificanceExcess nitrogen (N) in freshwaters is problematic due to its impacts on eutrophication, biodiversity losses, and harmful algal blooms. Some microbial processes such as denitrification and anammox can remove N from systems while others such as N-fixation can add a usable form of N. However, not enough is known about when and where these competing processes are occurring in lakes, and understanding this can provide insight to management. Here, we determined that nearly all of the 34 lakes that we examined in the upper Midwest had a net loss of N2 that must be compensated by watershed inputs to maintain steady state. These results suggest that N-fixation in these lakes was not enough to offset denitrification and anammox. Little is known about the exchange of gaseous nitrogen (N2) with the atmosphere in freshwater systems. Although the exchange of N2, driven by excess or deficiencies relative to saturation values, has little relevance to the atmospheric N2 pool due to its large size, it does play an important role in freshwater and marine nitrogen (N) cycling. N-fixation converts N2 to ammonia, which can be used by microbes and phytoplankton, while denitrification/anammox effectively removes it by converting oxidized, inorganic N to N2. We examined N2 saturation to infer net biological nitrogen processes in 34 lakes across 5° latitude varying in trophic status, mixing regime, and bathymetry. Here, we report that nearly all lakes examined in the upper Midwest (USA) were supersaturated with N2 (>85% of samples, n = 248), suggesting lakes are continuously releasing nitrogen to the atmosphere. The traditional paradigm is that freshwaters compensate for N-limitation through N-fixation, but these results indicate that lakes were constantly losing N to the atmosphere via denitrification and/or anammox, suggesting that terrestrial N inputs are needed to balance the internal N cycle.

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.

Freshwaters are significant contributors of greenhouse gases to the atmosphere, including carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O). Small waterbodies such as ponds are now recognized to have disproportionate greenhouse gas emissions relative to their size, but measured emissions from ponds have varied by several orders of magnitude. To assess drivers of variation in pond greenhouse gas dynamics, we measured concentrations and emissions of CO2, CH4, and N2O across 26 ponds in Minnesota, United States, during the ice-free season. The studied ponds differed in land-use, from urban stormwater ponds to natural forested ponds. The ponds were all sources of greenhouse gases, driven by large CH4 emissions (mean 704 [sd 840] mg CH4-C m−2 d−1). CO2 fluxes were variable, but on average a sink (mean −25.9 [sd 862] mg CO2-C m−2 d−1), and N2O emissions were generally low (mean 0.398 [sd 0.747] mg N2O-N m−2 d−1). Duckweed coverage on the water surfaces ranged from 0% to 100% coverage, and had the largest influence on water chemistry and greenhouse gas dynamics across the ponds. Duckweed covered ponds (ponds with greater than 85% coverage) had higher phosphorus levels and increased anoxia compared to ponds without duckweed (ponds with less than 12% coverage), leading to higher CH4 concentrations and overall greenhouse gas emissions in the duckweed ponds. Duckweed ponds had a mean emission rate in CO2 equivalents of 30.9 g C m−2 d−1 compared to 11.0 g C m−2 d−1 in non-duckweed ponds.

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 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.

The elemental content of microbial communities is dependent upon the physiology of constituent populations, yet ecological stoichiometry has made slow progress toward identifying predictors of how species and strains change the elemental content of their biomass in response to the stoichiometry of elements in resources. We asked whether the elemental content of aquatic bacteria, especially flexibility in elemental content, could be predicted by their phylogeny, maximum growth rate or lake productivity. We examined 137 isolates using chemostats and found that strains differed substantially in how the carbon:nitrogen:phosphorus ratios (C:N:P) in their biomass responded to P-sufficient and P-limiting conditions. The median strain increased its biomass C:N:P from 68:14:1 to 164:25:1 under P limitation. Patterns in elemental content and ratios were partly explained by phylogeny, yet flexibility in elemental content showed no phylogenetic signal. The growth rate hypothesis predicts that P content is positively related to growth rate, but we found weak correlation between maximum growth rate and P content among the strains. Overall, isolates from highly productive lakes had higher maximum growth rates and less flexible biomass N:P than isolates from unproductive lakes. These results show that bacteria present within lake communities exhibit diverse strategies for responding to elemental imbalance.