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Local biodiversity patterns are expected to strongly reflect variation in topography, land use, dispersal boundaries, nutrient supplies, contaminant spread, management practices, and other anthropogenic influences. Contrary to this expectation, studies focusing on specific taxa revealed a biodiversity homogenization effect in areas subjected to long‐term intensive industrial agriculture. We investigated whether land use affects biodiversity levels and community composition (α‐ and β‐diversity) in 67 kettle holes (KH) representing small aquatic islands embedded in the patchwork matrix of a largely agricultural landscape comprising grassland, forest, and arable fields. These KH, similar to millions of standing water bodies of glacial origin, spread across northern Europe, Asia, and North America, are physico‐chemically diverse and differ in the degree of coupling with their surroundings. We assessed aquatic and sediment biodiversity patterns of eukaryotes, Bacteria, and Archaea in relation to environmental features of the KH, using deep‐amplicon‐sequencing of environmental DNA (eDNA). First, we asked whether deep sequencing of eDNA provides a representative picture of KH aquatic biodiversity across the Bacteria, Archaea, and eukaryotes. Second, we investigated if and to what extent KH biodiversity is influenced by the surrounding land use. We hypothesized that richness and community composition will greatly differ in KH from agricultural land use compared with KH in grasslands and forests. Our data show that deep eDNA amplicon sequencing is useful for in‐depth assessments of cross‐domain biodiversity comprising both micro‐ and macro‐organisms, but has limitations with respect to single‐taxa conservation studies. Using this broad method, we show that sediment eDNA, integrating several years to decades, depicts the history of agricultural land‐use intensification. Aquatic biodiversity was best explained by seasonality, whereas land‐use type explained little of the variation. We concluded that, counter to our hypothesis, land use intensification coupled with landscape wide nutrient enrichment (including atmospheric deposition), groundwater connectivity between KH and organismal (active and passive) dispersal in the tight network of ponds, resulted in a biodiversity homogenization in the KH water, leveling off today's detectable differences in KH biodiversity between land‐use types. These findings have profound implications for measures and management strategies to combat current biodiversity loss in agricultural landscapes worldwide. [ABSTRACT FROM AUTHOR]

Many inland waters exhibit complete or partial desiccation, or have vanished due to global change, exposing sediments to the atmosphere. Yet, data on carbon dioxide (CO2) emissions from these sediments are too scarce to upscale emissions for global estimates or to understand their fundamental drivers. Here, we present the results of a global survey covering 196 dry inland waters across diverse ecosystem types and climate zones. We show that their CO2 emissions share fundamental drivers and constitute a substantial fraction of the carbon cycled by inland waters. CO2 emissions were consistent across ecosystem types and climate zones, with local characteristics explaining much of the variability. Accounting for such emissions increases global estimates of carbon emissions from inland waters by 6% (~0.12 Pg C y−1). Our results indicate that emissions from dry inland waters represent a significant and likely increasing component of the inland waters carbon cycle. Many inland waters seasonally or permanently dry up, thus exposing sediments to the atmosphere. Here the authors show that a substantial amount of CO2 is emitted from these dry sediments, increasing current inland water carbon flux estimates by 6%. [ABSTRACT FROM AUTHOR]

Cyanobacterial mass developments impact the community composition of heterotrophic microorganisms with far-reaching consequences for biogeochemical and energy cycles of freshwater ecosystems including reservoirs. Here we sought to evaluate the temporal stability of methanogenic archaea in the water column and further scrutinize their associations with cyanobacteria. Monthly samples were collected from October 2009 to December 2010 in hypereutrophic Pampulha reservoir with permanently blooming cyanobacteria, and from January to December 2011 in oligotrophic Volta Grande reservoir with only sporadic cyanobacteria incidence. The presence of archaea in cyanobacterial cultures was investigated by screening numerous strains of Microcystis spp. from these reservoirs as well as from lakes in Europe, Asia, and North-America. We consistently determined the occurrence of archaea, in particular methanogenic archaea, in both reservoirs throughout the year. However, archaea were only associated with two strains (Microcystis sp. UFMG 165 and UFMG 175) recently isolated from these reservoirs. These findings do not implicate archaea in the occurrence of methane in the epilimnion of inland waters, but rather serve to highlight the potential of microhabitats associated with particles, including phytoplankton, to shelter unique microbial communities. [ABSTRACT FROM AUTHOR]

Recent reports of increasing iron (Fe) concentrations in freshwaters are of concern, given the fundamental role of Fe in biogeochemical processes. Still, little is known about the frequency and geographical distribution of Fe trends or about the underlying drivers. We analyzed temporal trends of Fe concentrations across 340 water bodies distributed over 10 countries in northern Europe and North America in order to gain a clearer understanding of where, to what extent, and why Fe concentrations are on the rise. We found that Fe concentrations have significantly increased in 28% of sites, and decreased in 4%, with most positive trends located in northern Europe. Regions with rising Fe concentrations tend to coincide with those with organic carbon (OC) increases. Fe and OC increases may not be directly mechanistically linked, but may nevertheless be responding to common regional-scale drivers such as declining sulfur deposition or hydrological changes. A role of hydrological factors was supported by covarying trends in Fe and dissolved silica, as these elements tend to stem from similar soil depths. A positive relationship between Fe increases and conifer cover suggests that changing land use and expanded forestry could have contributed to enhanced Fe export, although increases were also observed in nonforested areas. We conclude that the phenomenon of increasing Fe concentrations is widespread, especially in northern Europe, with potentially significant implications for wider ecosystem biogeochemistry, and for the current browning of freshwaters. [ABSTRACT FROM AUTHOR]

Ecosystems are generally linked via fluxes of nutrients and energy across their boundaries. For example, freshwater ecosystems in temperate regions may receive significant inputs of terrestrially derived carbon via autumnal leaf litter. This terrestrial particulate organic carbon (POC) is hypothesized to subsidize animal production in lakes, but direct evidence is still lacking. We divided two small eutrophic lakes each into two sections and added isotopically distinct maize litter to the treatment sections to simulate increased terrestrial POC inputs via leaf litter in autumn. We quantified the reliance of aquatic consumers on terrestrial resources (allochthony) in the year subsequent to POC additions by applying mixing models of stable isotopes. We also estimated lake-wide carbon (C) balances to calculate the C flow to the production of the major aquatic consumer groups: benthic macroinvertebrates, crustacean zooplankton, and fish. The sum of secondary production of crustaceans and benthic macroinvertebrates supported by terrestrial POC was higher in the treatment sections of both lakes. In contrast, total secondary and tertiary production (supported by both autochthonous and allochthonous C) was higher in the reference than in the treatment sections of both lakes. Average aquatic consumer allochthony per lake section was 27-40%, although terrestrial POC contributed less than about 10% to total organic C supply to the lakes. The production of aquatic consumers incorporated less than 5% of the total organic C supply in both lakes, indicating a low ecological efficiency. We suggest that the consumption of terrestrial POC by aquatic consumers facilitates a strong coupling with the terrestrial environment. However, the high autochthonous production and the large pool of autochthonous detritus in these nutrient-rich lakes make terrestrial POC quantitatively unimportant for the C flows within food webs. [ABSTRACT FROM AUTHOR]

Studies investigating the effect of increasing CO2 levels on the phosphorus cycle in natural waters are lacking although phosphorus often controls phytoplankton development in aquatic systems. The aim of our study was to analyze effects of elevated CO2 levels on phosphorus pool sizes and uptake. Therefore, we conducted a CO2-manipulation mesocosm experiment in the Storfjärden (western Gulf of Finland, Baltic Sea) in summer 2012. We compared the phosphorus dynamics in different mesocosm treatments but also studied them outside the mesocosms in the surrounding fjord water. In the mesocosms as well as in surface waters of Storfjärden, dissolved organic phosphorus (DOP) concentrations of 0.26 ± 0.03 and 0.23 ± 0.04 μmol L−1, respectively, formed the main fraction of the total P-pool (TP), whereas phosphate (PO4) constituted the lowest fraction with mean concentration of 0.15 ± 0.02 μmol L−1 and 0.17 ± 0.07 μmol L−1 in the mesocosms and in the fjord, respectively. Uptake of PO4 ranged between 0.6 and 3.9 nmol L−1 h−1 of which ~ 86% (mesocosms) and ~ 72% (fjord) were realized by the size fraction < 3 μm. Adenosine triphosphate (ATP) uptake revealed that additional P was supplied from organic compounds accounting for 25–27% of P provided by PO4 only. CO2 additions did not cause significant changes in phosphorus (P) pool sizes, DOP composition, and uptake of PO4 and ATP when the whole study period was taken into account. About 18% of PO4 was transformed into POP, whereby the major proportion (~ 82%) was converted into DOP suggesting that the conversion of PO4 to DOP is the main pathway of the PO4 turnover. We observed that significant relationships (e.g., between POP and Chl a) in the untreated mesocosms vanished under increased fCO2 conditions. Consequently, it can be hypothesized that the relationship between POP formation and phytoplankton growth changed under elevated CO2 conditions. Significant short-term effects were observed for PO4 and particulate organic phosphorus (POP) pool sizes in CO2 treatments > 1000 µatm during periods when phytoplankton started to grow. [ABSTRACT FROM AUTHOR]

In the original version panel 2a is displayed in order of increasing percent I Microcystis i in the community, but the order of the histograms in panel 2b is not. (b) Relative abundance of non-Microcystis (i.e., microbiome) bacterial classes. gl In the updated figure the order has been corrected so the lake names on the x-axis now apply correctly to both panels. The lakes are arranged in order from left to right of increasing percent Microcystis in the community. [Extracted from the article]

Dissolved organic carbon (DOC) concentrations -- mainly of terrestrial origin -- are increasing worldwide in inland waters. The biodegradability of the DOC varies depending on quantity and chemical quality. Heterotrophic bacteria are the main consumers of DOC and thus determine DOC temporal dynamics and availability for higher trophic levels. It is therefore crucial to understand the processes controlling the bacterial turnover of additional allochthonous and autochthonous DOC in aquatic systems. Our aim was to study bacterial carbon (C) turnover with respect to DOC quantity and chemical quality using both allochthonous and autochthonous DOC sources. We incubated a natural bacterial community with allochthonous C (13C-labeled beech leachate) and increased concentrations and pulses (intermittent occurrence of organic matter input) of autochthonous C (algae lysate). We then determined bacterial carbon consumption, activities, and community composition together with the carbon flow through bacteria using stable C isotopes. The chemical analysis of single sources revealed differences in aromaticity and fractions of low and high molecular weight substances (LMWS and HMWS, respectively) between allochthonous and autochthonous C sources. In parallel to these differences in chemical composition, we observed a higher availability of allochthonous C as evidenced by increased DOC consumption and bacterial growth efficiencies (BGE) when solely allochthonous C was provided. In treatments with mixed sources, rising concentrations of added autochthonous DOC resulted in a further, significant increase in bacterial DOC consumption from 52 to 68% when nutrients were not limiting. This rise was accompanied by a decrease in the humic substances (HS) fraction and an increase in bacterial biomass. Stable C isotope analyses of phospholipid fatty acids (PLFA) and respired dissolved inorganic carbon (DIC) supported a preferential assimilation of autochthonous C and respiration of the allochthonous C. Changes in DOC concentration and consumption in mixed treatments did not affect bacterial community composition (BCC), but BCC differed in single vs. mixed incubations. Our study highlights that DOC quantity affects bacterial C consumption but not BCC in nutrient-rich aquatic systems. BCC shifted when a mixture of allochthonous and autochthonous C was provided simultaneously to the bacterial community. Our results indicate that chemical quality rather than source of DOC per se (allochthonous vs. autochthonous) determines bacterial DOC turnover. [ABSTRACT FROM AUTHOR]

Heterocystous cyanobacteria of the genus Nodularia form extensive blooms in the Baltic Sea and contribute substantially to the total annual primary production. Moreover, they dispense a large fraction of new nitrogen to the ecosystem when inorganic nitrogen concentration in summer is low. Thus, it is of ecological importance to know how Nodularia will react to future environmental changes, in particular to increasing carbon dioxide (CO 2) concentrations and what consequences there might arise for cycling of organic matter in the Baltic Sea. Here, we determined carbon (C) and dinitrogen (N 2) fixation rates, growth, elemental stoichiometry of particulate organic matter and nitrogen turnover in batch cultures of the heterocystous cyanobacterium Nodularia spumigena under low (median 315 µatm), mid (median 353 µatm), and high (median 548 µatm) CO2 concentrations. Our results demonstrate an overall stimulating effect of rising pCO 2 on C and N 2 fixation, as well as on cell growth. An increase in pCO 2 during incubation days 0 to 9 resulted in an elevation in growth rate by 84 ±38% (low vs. high pCO 2) and 40 ±25% (mid vs. high pCO 2), as well as in N 2 fixation by 93±35% and 38 ±1%, respectively. C uptake rates showed high standard deviations within treatments and in between sampling days. Nevertheless, C fixation in the high pCO 2 treatment was elevated compared to the other two treatments by 97% (high vs. low) and 44% (high vs. mid) at day 0 and day 3, but this effect diminished afterwards. Additionally, elevation in carbon to nitrogen and nitrogen to phosphorus ratios of the particulate biomass formed (POC : POP and PON: POP) was observed at high pCO 2. Our findings suggest that rising pCO 2 stimulates the growth of heterocystous diazotrophic cyanobacteria, in a similar way as reported for the non-heterocystous diazotroph Trichodesmium. Implications for biogeochemical cycling and food web dynamics, as well as ecological and socio-economical aspects in the Baltic Sea are discussed. [ABSTRACT FROM AUTHOR]

Heterocystous cyanobacteria of the genus Nodularia form extensive blooms in the Baltic Sea contributing substantially to the total annual primary production. Moreover, they dispense a large fraction of new nitrogen to the ecosystem, when inorganic nitrogen concentration in summer is low. Thus, it is of great ecological importance to know how Nodularia will react to future environmental changes, in particular to increasing carbon dioxide (CO2) concentrations and what consequences there might arise for cycling of organic matter in the ocean. Here, we determined carbon (C) and dinitrogen (N2) fixation rates, growth, elemental stoichiometry of particulate organic matter and nitrogen turnover during batch growth of the heterocystous cyanobacterium Nodularia spumigena under glacial (180 ppm), present (380 ppm), and future (780 ppm) CO2 concentrations. Our results demonstrate an overall stimulating effect of rising pCO2 on C2 and N2 fixation, as well as on cell growth. An increase in pCO2 resulted in an elevation in growth rate, C and N2 fixation by 23%, 36% and 25%, respectively (180 ppm vs. 380 ppm) and by 27%, 2% and 4%, respectively (380 ppm vs. 780 ppm). Additionally, elevation in the carbon and nitrogen to phosphorus quota of the particulate biomass formed (POC:POP and PON:POP) was observed at high pCO2. Our findings suggest that rising pCO2 stimulates the growth of heterocystous diazotrophic cyanobacteria, in a similar way as reported for non-heterocystous diazotrophs. Implications for biogeo-chemical cycling and food web dynamics, as well as ecological and socio-economical aspects in the Baltic Sea are discussed. [ABSTRACT FROM AUTHOR]

The predicted rise in anthropogenic CO2 emissions will increase CO2 concentrations and decrease seawater pH in the upper ocean. Recent studies have revealed effects of pCO2 induced changes in seawater chemistry on a variety of marine life forms, in particular calcifying organisms. To test whether the predicted increase in pCO2 will directly or indirectly (via changes in phytoplankton dynamics) affect abundance, activities, and community composition of heterotrophic bacteria during phytoplankton bloom development, we have aerated mesocosms with CO2 to obtain triplicates with three different partial pressures of CO2 (pCO2): 350 µatm (1 × CO2), 700 µatm (2 × CO2) and 1050 µatm (3 × CO2). The development of a phytoplankton bloom was initiated by the addition of nitrate and phosphate. In accordance to an elevated carbon to nitrogen drawdown at increasing pCO2, bacterial production (BPP) of free-living and attached bacteria as well as cell-specific BPP (csBPP) of attached bacteria were related to the C:N ratio of suspended matter. These relationships significantly differed among treatments. However, bacterial abundance and activities were not statistically different among treatments. Solely community structure of free-living bacteria changed with pCO2 whereas that of attached bacteria seemed to be independent of pCO2 but tightly coupled to phytoplankton bloom development. Our findings imply that changes in pCO2, although reflected by changes in community structure of free-living bacteria, do not directly affect bacterial activity. Furthermore, bacterial activity and dynamics of heterotrophic bacteria, especially of attached bacteria, were tightly correlated to phytoplankton development and, hence, may also potentially depend on changes in pCO2. [ABSTRACT FROM AUTHOR]

Availability of phosphate for phytoplankton and bacteria and of glucose for bacteria at different pCO2 levels were studied in a mesocosm experiment (PeECE III). Using nutrient-depleted SW Norwegian fjord waters, three different levels of pCO2 (350 μatm: 1×CO2; 700μatm: 2×CO2; 1050μatm: 3×CO2) were set up, and nitrate and phosphate were added at the start of the experiment in order to induce a phytoplankton bloom. Despite similar responses of total particulate P concentration and phosphate turnover time at the three different pCO2 levels, the size distribution of particulate P and 33PO4 uptake suggested that phosphate transferred to the >10μm fraction was greater in the 3×CO2 mesocosm during the first 6-10 days when phosphate concentration was high. During the period of phosphate depletion (after Day 12), specific phosphate affinity and specific alkaline phosphatase activity (APA) suggested a P-deficiency (i.e. suboptimal phosphate supply) rather than a P-limitation for the phytoplankton and bacterial community at the three different pCO2 levels. Specific phosphate affinity and specific APA tended to be higher in the 3×CO2 than in the 2×CO2 and 1×CO2 mesocosms during the phosphate depletion period, although no statistical differences were found. Glucose turnover time was correlated significantly and negatively with bacterial abundance and production but not with the bulk DOC concentration. This suggests that even though constituting a small fraction of the bulk DOC, glucose was an important component of labile DOC for bacteria. Specific glucose affinity of bacteria behaved similarly at the three different pCO2 levels with measured specific glucose affinities being consistently much lower than the theoretical maximum predicted from the diffusion-limited model. This suggests that bacterial growth was not severely limited by the glucose availability. Hence, it seems that the lower availability of inorganic nutrients after the phytoplankton bloom reduced the bacterial capacity to consume labile DOC in the upper mixed layer of the stratified mesocosms. [ABSTRACT FROM AUTHOR]

Using 15N and 33P, we measured the turnover of organic and inorganic nitrogen (N) and phosphorus (P) substrates, and the partitioning of N and P from these sources into two size fractions of marine osmotrophs during the course of a phytoplankton bloom in a nutrient manipulated mesocosm. The larger size fraction (>0.8 μm), mainly consisting of the coccolithophorid Emiliania huxleyi, but also including an increasing amount of large particle-associated bacteria as the bloom proceeded, dominated uptake of the inorganic forms NH+4 , NO-3 , and PO3-4 . The uptake of N from leucine, and P from ATP and dissolved DNA, was initially dominated by the 0.8-0.2 μm size fraction, but shifted towards dominance by the >0.8 μm size fraction as the system turned to an increasing degree of N-deficiency. Normalizing uptake to biomass of phytoplankton and heterotrophic bacteria revealed that organisms in the 0.8-0.2 μm size fraction had higher specific affinity for leucine-N than those in the >0.8 μm size fraction when N was deficient, whereas the opposite was the case for NH+4 . There was no such difference regarding the specific affinity for P substrates. Since heterotrophic bacteria seem to acquire N from organic compounds like leucine more efficiently than phytoplankton, our results suggest different structuring of the microbial food chain in N-limited relative to P-limited environments. [ABSTRACT FROM AUTHOR]

The predicted rise in anthropogenic CO2 emissions will increase CO2 concentrations and decrease seawater pH in the upper ocean. Recent studies have revealed effects of pCO2 induced changes in seawater chemistry on a variety of marine life forms, in particular calcifying organisms. To test whether the predicted increase in pCO2 will directly or indirectly (via changes in phytoplankton dynamics) affect abundance, activities, and community composition of heterotrophic bacteria during phytoplankton bloom development, we have aerated mesocosms with CO2 to obtain triplicates with three different partial pressures of CO2 (pCO2): 350 μatm (1×CO2), 700 μatm (2×CO2) and 1050 μatm (3×CO2). The development of a phytoplankton bloom was initiated by the addition of nitrate and phosphate. In accordance to an elevated carbon to nitrogen drawdown at increasing pCO2, bacterial production (BPP) of free-living and attached bacteria as well as cell-specific BPP (csBPP) of attached bacteria were related to the C:N ratio of suspended matter. These relationships significantly differed among treatments. However, bacterial abundance and activities were not statistically different among treatments. Solely community structure of free-living bacteria changed with pCO2 whereas that of attached bacteria seemed to be independent of pCO2 but tightly coupled to phytoplankton bloom development. Our findings imply that changes in pCO2, although reflected by changes in community structure of free-living bacteria, do not directly affect bacterial activity. Furthermore, bacterial activity and dynamics of heterotrophic bacteria, especially of attached bacteria, were tightly linked to phytoplankton development and, hence, may also potentially depend on changes in pCO2. [ABSTRACT FROM AUTHOR]

Availability of phosphate for phytoplankton and bacteria and of labile organic carbon for bacteria at different pCO2 levels were studied in a mesocosm experiment (PeECE III). Using nutrient-depleted SW Norwegian fjord waters, three different levels of pCO2 (350 μatm: 1×CO2; 750 μatm: 2×CO2; 1050 μatm: 3×CO2) were set up, and nitrate and phosphate were added at the start of the experiment in order to induce a phytoplankton bloom. Despite similar responses of total particulate P concentration and phosphate turnover time at the three different pCO2 levels, the size distribution of particulate P and 33PO4 uptake suggested that phosphate transferred to the >10 μm fraction was greater in the 3×CO2 mesocosm during the first 6-10 days when phosphate concentration was high. During the period of phosphate depletion (after Day 12), specific phosphate affinity and specific alkaline phosphatase activity (APA) suggested a P-deficiency (i.e. suboptimal phosphate supply) but not a P-limitation for the phytoplankton and bacterial community at the three different pCO2 levels. Although specific phosphate affinity and specific APA tended to be higher in 3×CO2 than in 2×CO2 and 1×CO2 mesocosms during the phosphate depletion period, no statistical differences were found. Responses of specific glucose affinity for bacteria were similar at the three different pCO2 levels. Measured specific glucose affinities were consistently much lower than the theoretical maximum predicted from the diffusion-limited model, suggesting that bacterial growth was not limited by the availability of labile dissolved organic carbon. These results suggest that availability of phosphate and glucose was similar at the three different pCO2 levels. [ABSTRACT FROM AUTHOR]

Using 15N and 33P, we measured the turnover of organic and inorganic nitrogen (N) and phosphorus (P) substrates, and the partitioning of N and P from these sources into two size fractions of marine osmotrophs during the course of a phytoplankton bloom in a nutrient manipulated mesocosm. The larger size fraction (>0.8 µm), mainly consisting of the coccolithophorid Emiliania huxleyi, but also including an increasing amount of large particle-associated bacteria as the bloom proceeded, dominated uptake of the inorganic forms NH4+ , NO3- , and PO43- . The uptake of N from leucine, and P from ATP and dissolved DNA (dDNA), was initially dominated by the 0.8-0.2 µm size fraction, but shifted towards dominance by the >0.8 µm size fraction as the system turned to an increasing degree of N-deficiency. Normalizing uptake to biomass of phytoplankton and heterotrophic bacteria revealed that organisms in the 0.8-0.2 µm size fraction had higher specific affinity for leucine-N than those in the >0.8 µm size fraction when N was deficient, whereas the opposite was the case for NH4+ . There was no such difference regarding the specific affinity for P substrates. Since heterotrophic bacteria seem to acquire N from organic compounds like leucine more efficiently than phytoplankton, our results suggest different structuring of the microbial food chain in N-limited relative to P-limited environments. [ABSTRACT FROM AUTHOR]