Long-Term m5C Methylome Dynamics Parallel Phenotypic Adaptation in the Cyanobacterium Trichodesmium

A major challenge in modern biology is understanding how the effects of short-term biological responses influence long-term evolutionary adaptation, defined as a genetically determined increase in fitness to novel environments. This is particularly important in globally important microbes experiencing rapid global change, due to their influence on food webs, biogeochemical cycles, and climate. Epigenetic modifications like methylation have been demonstrated to influence short-term plastic responses, which ultimately impact long-term adaptive responses to environmental change. However, there remains a paucity of empirical research examining long-term methylation dynamics during environmental adaptation in nonmodel, ecologically important microbes. Here, we show the first empirical evidence in a marine prokaryote for long-term m5C methylome modifications correlated with phenotypic adaptation to CO₂, using a 7-year evolution experiment (1,000+ generations) with the biogeochemically important marine cyanobacterium Trichodesmium. We identify m5C methylated sites that rapidly changed in response to high (750 µatm) CO₂ exposure and were maintained for at least 4.5 years of CO₂ selection. After 7 years of CO₂ selection, however, m5C methylation levels that initially responded to high-CO₂ returned to ancestral, ambient CO₂ levels. Concurrently, high-CO₂ adapted growth and N₂ fixation rates remained significantly higher than those of ambient CO₂ adapted cell lines irrespective of CO₂ concentration, a trend consistent with genetic assimilation theory. These data demonstrate the maintenance of CO₂-responsive m5C methylation for 4.5 years alongside phenotypic adaptation before returning to ancestral methylation levels. These observations in a globally distributed marine prokaryote provide critical evolutionary insights into biogeochemically important traits under global change.     

Community composition has greater impact on the functioning of marine phytoplankton communities than ocean acidification

Ecosystem functioning is simultaneously affected by changes in community composition and environmental change such as increasing atmospheric carbon dioxide (CO₂) and subsequent ocean acidification. However, it largely remains uncertain how the effects of these factors compare to each other. Addressing this question, we experimentally tested the hypothesis that initial community composition and elevated CO₂ are equally important to the regulation of phytoplankton biomass. We full‐factorially exposed three compositionally different marine phytoplankton communities to two different CO₂ levels and examined the effects and relative importance (ω²) of the two factors and their interaction on phytoplankton biomass at bloom peak. The results showed that initial community composition had a significantly greater impact than elevated CO₂ on phytoplankton biomass, which varied largely among communities. We suggest that the different initial ratios between cyanobacteria, diatoms, and dinoflagellates might be the key for the varying competitive and thus functional outcome among communities. Furthermore, the results showed that depending on initial community composition elevated CO₂ selected for larger sized diatoms, which led to increased total phytoplankton biomass. This study highlights the relevance of initial community composition, which strongly drives the functional outcome, when assessing impacts of climate change on ecosystem functioning. In particular, the increase in phytoplankton biomass driven by the gain of larger sized diatoms in response to elevated CO₂ potentially has strong implications for nutrient cycling and carbon export in future oceans.     

气候和土地利用变化影响下生态屏障带水土流失趋势研究

受气候和地形等诸多因素影响，我国"两屏三带"国家生态屏障带中的川滇-黄土高原区域和南方丘陵带水土流失十分严重，自然灾害频发。但是，针对川滇-黄土高原区域和南方丘陵带水土流失时空格局变化，特别是未来气候变化和土地利用变化影响下水土流失变化趋势的研究很少。因此，本研究以川滇-黄土高原区域和南方丘陵带为研究对象，利用修正土壤流失方程（RUSLE）定量分析了该区在2000-2015年水土流失的时空变化规律及其影响因素，并预测了在RCP2.6和RCP4.5的未来气候情景下及土地利用变化条件下水土流失的变化趋势。研究结果表明：（1）黄土高原地区在植被恢复的积极作用下，水土流失显著缓解；（2）川滇地区的西南部因植被盖度的增长和降雨的减少水土流失显著缓解，但四川省境内人口密集区农田面积增加以及降水增加造成水土流失大幅度加剧；（3）南方丘陵带受降水增加影响导致了部分区域的水土流失恶化；（4）在未来气候变化情景下，由于大部分地区降雨将减少使土壤侵蚀趋于缓解，但四川、黄土高原和南方丘陵带大部分地区仍然面临未来农田面积增加带来的水土侵蚀压力。考虑到未来气候变化情景下降雨减少的趋势，建议在黄土高原地区提高草地在土地利用类型中的占比，在减少耗水量的同时维持地表盖度，缓解水土侵蚀；此外，各区域仍需控制农田面积，而且需通过加强坡耕地上保水保土耕作措施降低农田区域的土壤侵蚀压力。     

Landscape-level seagrass–sediment relations in a coastal lagoon

We investigated the relationships between sediment (subaqueous soil) properties and eelgrass (Zostera marina L.) distribution to develop landscape-level soil-based strategies for choosing eelgrass restoration locations. Subaqueous soils were sampled and eelgrass cover determined for 14 soil-landscape units within a 116 ha area of Ninigret Pond, a coastal lagoon in Rhode Island, USA. Of the 14 soil-landscape units sampled for eelgrass cover, 52% had virtually no eelgrass cover (<10%), while 18% had high eelgrass cover (>90%). The Lagoon Bottom, Shallow Lagoon Bottom, Flood-tidal Delta Slope, and Barrier Cove subaqueous soil-landscape units had the highest eelgrass cover (66–100%). A weak relationship between eelgrass cover and water depths (r² = 0.10) was observed suggesting that properties other than water depth may also control eelgrass distribution. Subaqueous soils on landscapes with >60% eelgrass cover had relatively high levels of acid-volatile sulfides (>90 μg/g), high soil salinity levels (34–44 ppt), fine textures (silt loam), and relatively high total nitrogen levels (>0.15%). Four principal components accounted for 81% of the variability in eelgrass cover. The first component reflected particle-size distribution (i.e. sand, silt, and clay contents) effects and accounted for 43% of the variability. The other components suggested that eelgrass cover is correlated to carbonaceous remains, non-calcareous rock fragments and soil salinity. These data suggest that the current distribution of eelgrass within the study area is strongly influenced by physical and chemical subaqueous soil characteristics. Soil survey techniques proved useful for the delineation of sediment characteristics (e.g. texture, salinity) that influence eelgrass distribution patterns at landscape-level scales.     

A sensitive method for continuous measurement of the carbon dioxide evolution rate of soil samples

Summary A differential infrared CO₂ analyser combined with a 12 channel gas handling system have been used for the measurement of CO₂ evolution rates of soil samples. A constant flow of air over the soil was maintained during the incubation period. Automatic sequential measurement and recording of the increase of the CO₂ content of the flushed air of the 12 channels lasted 24 min with a dwell time of 2 min per channel. This technique has proven to be very useful for accurate and rapid measurement of the biological activities in untreated and treated soil.     

Archaeorhizomyces borealis sp. nov. and a sequence-based classification of related soil fungal species

The class Archaeorhizomycetes (Taphrinomycotina, Ascomycota) was introduced to accommodate an ancient lineage of soil-inhabiting fungi found in association with plant roots. Based on environmental sequencing data Archaeorhizomycetes may comprise a significant proportion of the total fungal community in soils. Yet the only species described and cultivated in this class is Archaeorhizomyces finlayi. In this paper, we describe a second species from a pure culture, Archaeorhizomyces borealis NS99-600^T (=CBS138755^ExT) based on morphological, physiological, and multi-locus molecular characterization. Archaeorhizomyces borealis was isolated from a root tip of a Pinus sylvestris seedling grown in a forest nursery in Lithuania. Analysis of Archaeorhizomycete species from environmental samples shows that it has a Eurasian distribution and is the most commonly observed species. Archaeorhizomyces borealis shows slow growth in culture and forms yellowish creamy colonies, characteristics that distinguish A. borealis from its closest relative A. finlayi. Here we also propose a sequence-based taxonomic classification of Archaeorhizomycetes and predict that approximately 500 species in this class remain to be isolated and described.     

Does elevated pCO2 affect reef octocorals?

Increasing anthropogenic pCO₂ alters seawater chemistry, with potentially severe consequences for coral reef growth and health. Octocorals are the second most important faunistic component in many reefs, often occupying 50% or more of the available substrate. Three species of octocorals from two families were studied in Eilat (Gulf of Aqaba), comprising the zooxanthellate Ovabunda macrospiculata and Heteroxenia fuscescens (family Xeniidae), and Sarcophyton sp. (family Alcyoniidae). They were maintained under normal (8.2) and reduced (7.6 and 7.3) pH conditions for up to 5 months. Their biolological features, including protein concentration, polyp weight, density of zooxanthellae, and their chlorophyll concentration per cell, as well as polyp pulsation rate, were examined under conditions more acidic than normal, in order to test the hypothesis that rising pCO₂ would affect octocorals. The results indicate no statistically significant difference between the octocorals exposed to reduced pH values compared to the control. It is therefore suggested that the octocorals' tissue may act as a protective barrier against adverse pH conditions, thus maintaining them unharmed at high levels of pCO₂.     

Acetic acid and acidification accelerate chronological and replicative aging in yeast

Comment on: Murakami C, et al. Cell Cycle 2012; 11:3087-96.