Microbial species performance responses to environmental changes: genomic traits and nutrient availability

Ecology ◽  
2021 ◽  
Author(s):  
Ang Hu ◽  
Minglei Ren ◽  
Jianjun Wang
Keyword(s):  
Nutrient Availability ◽  
Environmental Changes ◽  
Microbial Species ◽  
Species Performance

scholarly journals Nutrient supply controls the linkage between species abundance and ecological interactions in marine bacterial communities

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Tianjiao Dai ◽  
Donghui Wen ◽  
Colin T. Bates ◽  
Linwei Wu ◽  
Xue Guo ◽  
...  
Keyword(s):  
Nutrient Availability ◽  
Copy Number ◽  
Abiotic Factors ◽  
Species Abundance ◽  
Coastal Sediment ◽  
Global Ocean ◽  
Bacterial Growth Rate ◽  
Opposite Pattern ◽  
Microbial Species ◽  
Rare Biosphere

AbstractNutrient scarcity is pervasive for natural microbial communities, affecting species reproduction and co-existence. However, it remains unclear whether there are general rules of how microbial species abundances are shaped by biotic and abiotic factors. Here we show that the ribosomal RNA gene operon (rrn) copy number, a genomic trait related to bacterial growth rate and nutrient demand, decreases from the abundant to the rare biosphere in the nutrient-rich coastal sediment but exhibits the opposite pattern in the nutrient-scarce pelagic zone of the global ocean. Both patterns are underlain by positive correlations between community-level rrn copy number and nutrients. Furthermore, inter-species co-exclusion inferred by negative network associations is observed more in coastal sediment than in ocean water samples. Nutrient manipulation experiments yield effects of nutrient availability on rrn copy numbers and network associations that are consistent with our field observations. Based on these results, we propose a “hunger games” hypothesis to define microbial species abundance rules using the rrn copy number, ecological interaction, and nutrient availability.

scholarly journals Phytoplankton dynamics in relation to environmental changes in a phytoplankton-dominated Mediterranean lagoon (Cabras Lagoon, Italy)

2012 ◽  
Vol 3 (2) ◽  
pp. 147 ◽  
Author(s):  
B.M. Padedda ◽  
S. Pulina ◽  
P. Magni ◽  
N. Sechi ◽  
A. Lugliè
Keyword(s):  
Nutrient Availability ◽  
Environmental Changes ◽  
Negative Impact ◽  
Inorganic Nitrogen ◽  
Algal Species ◽  
Temporal Variations ◽  
Extreme Weather Events ◽  
Economic Activities ◽  
Phytoplankton Assemblages ◽  
High Nutrient

In Mediterranean lagoons, macrophytes often surpass phytoplankton as the most important primary producers. Less frequently, phytoplankton dominates throughout the year, thus knowledge of its dynamics is relatively limited and scattered. In this study, we assessed over two years the dynamics of phytoplankton assemblages, including potential harmful algal species (HAS), in relation to environmental changes in the phytoplankton-dominated Cabras Lagoon (Sardinia, Italy). The lagoon was characterised by uniform spatial conditions, wide temporal variations in salinity (40 PSU) and high nutrient availability. Phosphorus was highest in summer, possibly recycled within the system, while dissolved inorganic nitrogen increased in winter and spring due to watershed discharge. Chlorophyll a, positively correlated with nutrients and rainfall, showed a typical bimodal pattern with summer-winter blooms. Modifications in phytoplankton composition strongly correlated with extreme weather events, such as intense rainfall. This generated an abrupt salinity decrease that, combined with high nutrient availability, favoured the dominance of Cyanophyceae of reduced cell size, such as Cyanobium and Rhabdoderma species. We suggest that the prolonged and intense dominance of Cyanophyceae, added to other HAS, has a negative impact on the primary economic activities of the lagoon, such as fishery, and generally on the whole lagoon functioning.

scholarly journals Can morphological features of coccolithophores serve as a reliable proxy to reconstruct environmental conditions of the past?

2019 ◽  
Author(s):  
Giulia Faucher ◽  
Ulf Riebesell ◽  
Lennart Thomas Bach
Keyword(s):  
Light Intensity ◽  
Nutrient Availability ◽  
Environmental Conditions ◽  
Environmental Changes ◽  
Morphological Changes ◽  
Specific Factor ◽  
Calcareous Nannofossils ◽  
Carbonate Chemistry ◽  
Common Response ◽  
Changing Light

Abstract. Morphological changes in coccoliths, tiny calcite platelets covering the outer surface of coccolithophores, can be the result of physiological responses to environmental changes. Coccoliths recovered from sedimentary successions may therefore provide information on paleo-environmental conditions prevailing at the time when the coccolithophores were alive. To calibrate the biomineralization responses of ancient coccolithophore to climatic changes studies often compared the biological responses of living coccolithophore species with paleo-data from calcareous nannofossils. However, there is uncertainty whether the morphological responses of living coccolithophores are representative for those of the fossilized ancestors. To investigate this, we cultured four living coccolithophore species (Emiliania huxleyi, Gephyrocapsa oceanica, Coccolithus pelagicus subsp. braarudii, and Pleurochrysis carterae) that have been evolutionarily distinct for millions of years, exposed them to changing environmental conditions (i.e. changing light intensity, Mg / Ca ratio, nutrient availability, temperature and carbonate chemistry) and evaluated their responses in coccolith morphology (i.e. size, length, width, malformation). The motivation for this study was that if the species show the same morphological response to changes in any of the tested abiotic environmental factors, then there is a reason to assume that this response is conserved over geological timescales and that coccolith morphology can serve as a paleo-proxy for that specific factor. In contrast with this concept, we found that the four species responded differently to changing light intensity, Mg / Ca ratio, nutrient availability and temperature in terms of coccolith morphology. The lack of a common response reveals the difficulties in using coccolith morphology as a proxy for paleo-environmental conditions. However, a common response was observed under changing seawater carbonate chemistry (i.e. rising CO2) which consistently induced malformations. This commonality provides some confidence that malformations found in the sedimentary record could be indicative for high CO2 levels.

scholarly journals Lysosome Sensing Is a Key Mechanism in Leishmania Intracellular Development

2021 ◽  
Vol 12 ◽  
Author(s):  
Dan Zilberstein
Keyword(s):  
Heat Shock ◽  
Protein Kinase ◽  
Body Temperature ◽  
Protein Kinase A ◽  
Nutrient Availability ◽  
Environmental Changes ◽  
Acidic Ph ◽  
Intracellular Form ◽  
Human Leishmaniasis ◽  
Kinase A

Phagolysosomes of macrophages are the niche where the parasitic protozoan Leishmania resides and causes human leishmaniasis. During infection, this organism encounters dramatic environmental changes. These include heat shock (from 26°C in the vector to 33°C or 37°C in the host, for cutaneous and visceral species, respectively) and acidic pH typical to the lysosome and nutrient availability. Leishmania cells developed ways to sense the lysosome-specific environment (acidic pH and body temperature) as means of recognition and, subsequently, initiation of differentiation into the intracellular form. Recent studies have indicated that protein kinase A plays a role as the gatekeeper that enables differentiation initiation. This review provides an update on the lysosome signaling pathway-mediated Leishmania intracellular development.

scholarly journals Can morphological features of coccolithophores serve as a reliable proxy to reconstruct environmental conditions of the past?

2020 ◽  
Vol 16 (3) ◽  
pp. 1007-1025 ◽  
Author(s):  
Giulia Faucher ◽  
Ulf Riebesell ◽  
Lennart Thomas Bach
Keyword(s):  
Light Intensity ◽  
Nutrient Availability ◽  
Environmental Conditions ◽  
Environmental Changes ◽  
Morphological Changes ◽  
Environmental Drivers ◽  
Specific Factor ◽  
Carbonate Chemistry ◽  
Common Response ◽  
Changing Light

Abstract. Morphological changes in coccoliths, tiny calcite platelets covering the outer surface of coccolithophores, can be induced by physiological responses to environmental changes. Coccoliths recovered from sedimentary successions may therefore provide information on paleo-environmental conditions prevailing at the time when the coccolithophores were alive. To calibrate the biomineralization responses of ancient coccolithophore to environmental changes, studies often compared the biological responses of living coccolithophore species with paleo-data from calcareous nannofossils. However, there is uncertainty whether the morphological responses of living coccolithophores are representative of those of the fossilized ancestors. To investigate this, we exposed four living coccolithophore species (Emiliania huxleyi, Gephyrocapsa oceanica, Coccolithus pelagicus subsp. braarudii, and Pleurochrysis carterae) that have been evolutionarily distinct for hundreds of thousands to millions of years, to a range of environmental conditions (i.e., changing light intensity, Mg∕Ca ratio, nutrient availability, temperature, and carbonate chemistry) and evaluated their responses in coccolith morphology (i.e., size, length, width, malformation). The motivation for this study was to test if there is a consistent morphological response of the four species to changes in any of the tested abiotic environmental factors. If this was the case, then this could suggest that coccolith morphology can serve as a paleo-proxy for that specific factor because this response is conserved across species that have been evolutionary distinct over geological timescales. However, we found that the four species responded differently to changing light intensity, Mg∕Ca ratio, nutrient availability, and temperature in terms of coccolith morphology. The lack of a common response reveals the difficulties in using coccolith morphology as a paleo-proxy for these environmental drivers. However, a common response was observed under changing seawater carbonate chemistry (i.e., rising CO2), which consistently induced malformations. This commonality provides some confidence that malformations found in the sedimentary record could be indicative of adverse carbonate chemistry conditions.

scholarly journals The influence of soil properties and nutrients on conifer forest growth in Sweden, and the first steps in developing a nutrient availability metric

2018 ◽  
Vol 15 (11) ◽  
pp. 3475-3496 ◽  
Author(s):  
Kevin Van Sundert ◽  
Joanna A. Horemans ◽  
Johan Stendahl ◽  
Sara Vicca
Keyword(s):  
Soil Properties ◽  
Tree Growth ◽  
Nutrient Availability ◽  
Environmental Changes ◽  
Forest Productivity ◽  
Forest Growth ◽  
International Institute ◽  
Soil Factors ◽  
Potential Productivity ◽  
Soil C

Abstract. The availability of nutrients is one of the factors that regulate terrestrial carbon cycling and modify ecosystem responses to environmental changes. Nonetheless, nutrient availability is often overlooked in climate–carbon cycle studies because it depends on the interplay of various soil factors that would ideally be comprised into metrics applicable at large spatial scales. Such metrics do not currently exist. Here, we use a Swedish forest inventory database that contains soil data and tree growth data for > 2500 forests across Sweden to (i) test which combination of soil factors best explains variation in tree growth, (ii) evaluate an existing metric of constraints on nutrient availability, and (iii) adjust this metric for boreal forest data. With (iii), we thus aimed to provide an adjustable nutrient metric, applicable for Sweden and with potential for elaboration to other regions. While taking into account confounding factors such as climate, N deposition, and soil oxygen availability, our analyses revealed that the soil organic carbon concentration (SOC) and the ratio of soil carbon to nitrogen (C : N) were the most important factors explaining variation in “normalized” (climate-independent) productivity (mean annual volume increment – m3 ha−1 yr−1) across Sweden. Normalized forest productivity was significantly negatively related to the soil C : N ratio (R2 = 0.02–0.13), while SOC exhibited an empirical optimum (R2 = 0.05–0.15). For the metric, we started from a (yet unvalidated) metric for constraints on nutrient availability that was previously developed by the International Institute for Applied Systems Analysis (IIASA – Laxenburg, Austria) for evaluating potential productivity of arable land. This IIASA metric requires information on soil properties that are indicative of nutrient availability (SOC, soil texture, total exchangeable bases – TEB, and pH) and is based on theoretical considerations that are also generally valid for nonagricultural ecosystems. However, the IIASA metric was unrelated to normalized forest productivity across Sweden (R2 = 0.00–0.01) because the soil factors under consideration were not optimally implemented according to the Swedish data, and because the soil C : N ratio was not included. Using two methods (each one based on a different way of normalizing productivity for climate), we adjusted this metric by incorporating soil C : N and modifying the relationship between SOC and nutrient availability in view of the observed relationships across our database. In contrast to the IIASA metric, the adjusted metrics explained some variation in normalized productivity in the database (R2 = 0.03–0.21; depending on the applied method). A test for five manually selected local fertility gradients in our database revealed a significant and stronger relationship between the adjusted metrics and productivity for each of the gradients (R2 = 0.09–0.38). This study thus shows for the first time how nutrient availability metrics can be evaluated and adjusted for a particular ecosystem type, using a large-scale database.

scholarly journals Local root growth and death are mediated by contrasts in nutrient availability and root quantity between soil patches

2018 ◽  
Vol 285 (1886) ◽  
pp. 20180699 ◽  
Author(s):  
Peng Wang ◽  
Yan Yang ◽  
Pu Mou ◽  
Qingzhou Zhao ◽  
Yunbin Li
Keyword(s):  
Root Growth ◽  
Nutrient Availability ◽  
Environmental Changes ◽  
Nutrient Status ◽  
Root Production ◽  
Solution Versus ◽  
Hoagland Solution ◽  
Contrast Condition ◽  
Whole Plant ◽  
Local Root

Plants are thought to be able to regulate local root growth according to its overall nutrient status as well as nutrient contents in a local substrate patch. Therefore, root plastic responses to environmental changes are probably co-determined by local responses of root modules and systematic control of the whole plant. Recent studies showed that the contrast in nutrient availability between different patches could significantly influence the growth and death of local roots. In this study, we further explored, beside nutrient contrast, whether root growth and death in a local patch are also affected by relative root quantity in the patch. We conducted a split-root experiment with different splitting ratios of roots of Canada goldenrod ( Solidago canadensis ) individuals, as well as high- (5× Hoagland solution versus water) or low- (1× Hoagland solution versus water) contrast nutrient conditions for the split roots. The results showed that root growth decreased in nutrient-rich patches but increased in nutrient-poor patches when more roots co-occurred in the same patches, irrespective of nutrient contrast condition. Root mortality depended on contrasts in both root quantity and nutrients: in the high-nutrient-contrast condition, it increased in nutrient-rich patches but decreased in nutrient-poor patches with increasing root proportion; while in the low-nutrient-contrast condition, it showed the opposite trend. These results demonstrated that root growth and death dynamics were affected by the contrast in both nutrient availability and root quantity between patches. Our study provided ecological evidence that local root growth and death are mediated by both the responses of root modules to a nutrient patch and the whole-plant nutrient status, suggesting that future work investigating root production and turnover should take into account the degree of heterogeneity in nutrient and root distribution.

scholarly journals The influence of soil properties and nutrients on conifer forest growth in Sweden, and the first steps in developing a nutrient availability metric

2017 ◽  
Author(s):  
Kevin Van Sundert ◽  
Joanna A. Horemans ◽  
Johan Stendahl ◽  
Sara Vicca
Keyword(s):  
Nutrient Availability ◽  
Environmental Changes ◽  
Forest Growth ◽  
Organic Carbon Content ◽  
Conifer Forest ◽  
Growth Data ◽  
Soil Factors ◽  
Ecosystem Responses ◽  
Soil C ◽  
The Relationship

Abstract. The availability of nutrients regulates terrestrial carbon cycling and modifies ecosystem responses to environmental changes. Nonetheless, nutrient availability is often overlooked in climate-carbon cycle studies because it depends on the interplay of various soil factors that would ideally be comprised into one metric. Such a metric does not currently exist. Here, we used a Swedish forest inventory database that contains soil and tree growth data for > 2500 forests across Sweden to test which combination soil factors best explains variation in plant growth, and to take the first steps in developing a nutrient availability metric. For the latter, we started from a (yet unvalidated) metric for constraints on nutrient availability that was previously developed by IIASA (Laxenburg, Austria). This IIASA-metric was developed for crops and uses only indirect indicators of nutrient availability. Our analyses revealed that soil organic carbon content (SOC) and the soil carbon to nitrogen (C : N) ratio were the most important factors explaining variation in normalized (climate-independent) productivity. Normalized productivity increased with decreasing soil C : N ratio (R2 = 0.02–0.13), while SOC exhibited an empirical optimum (R2 = 0.05–0.15). The IIASA-metric was unrelated to normalized productivity (R2 = 0.00–0.01), because the soil factors under consideration were not well implemented, and because the C : N ratio was not included. We upgraded this metric by incorporating soil C : N and adjusting the relationship between SOC and nutrient availability in view of the observed relationship across our database. This upgraded metric explained a significant fraction of the variation (R2 = 0.03–0.21; depending on the applied method) and thus opens up new opportunities to further validate and improve it with other datasets, from forests and from other ecosystem types, to ultimately develop a generic global nutrient availability metric.

Linking transcription, RNA polymerase II elongation and alternative splicing

2020 ◽  
Vol 477 (16) ◽  
pp. 3091-3104 ◽  
Author(s):  
Luciana E. Giono ◽  
Alberto R. Kornblihtt
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Rna Polymerase Ii ◽  
Environmental Changes ◽  
Transcription Elongation ◽  
Single Gene ◽  
Regulation Of Gene Expression ◽  
Regulation Of Transcription ◽  
Stepping Stones ◽  
Eukaryotic Transcription

Gene expression is an intricately regulated process that is at the basis of cell differentiation, the maintenance of cell identity and the cellular responses to environmental changes. Alternative splicing, the process by which multiple functionally distinct transcripts are generated from a single gene, is one of the main mechanisms that contribute to expand the coding capacity of genomes and help explain the level of complexity achieved by higher organisms. Eukaryotic transcription is subject to multiple layers of regulation both intrinsic — such as promoter structure — and dynamic, allowing the cell to respond to internal and external signals. Similarly, alternative splicing choices are affected by all of these aspects, mainly through the regulation of transcription elongation, making it a regulatory knob on a par with the regulation of gene expression levels. This review aims to recapitulate some of the history and stepping-stones that led to the paradigms held today about transcription and splicing regulation, with major focus on transcription elongation and its effect on alternative splicing.

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