scholarly journals Fungal genomes tell a story of ecological adaptations

2014 ◽  
Vol 10 ◽  
pp. 9-17
Author(s):  
Anna Muszewska

One genome enables a fungus to have various lifestyles and strategies depending on environmental conditions and in the presence of specific counterparts. The nature of their interactions with other living and abiotic elements is a consequence of their osmotrophism. The ability to degrade complex compounds and especially plant biomass makes them a key component of the global carbon circulation cycle. Since the first fungal genomic sequence was published in 1996 mycology has benefited from the technolgical progress. The available data create an unprecedented opportunity to perform massive comparative studies with complex study design variants targeted at all cellular processes.

Author(s):  
Muhammed Jamsheer K ◽  
Manoj Kumar ◽  
Vibha Srivastava

AbstractThe Snf1-related protein kinase 1 (SnRK1) is the plant homolog of the heterotrimeric AMP-activated protein kinase/sucrose non-fermenting 1 (AMPK/Snf1), which works as a major regulator of growth under nutrient-limiting conditions in eukaryotes. Along with its conserved role as a master regulator of sugar starvation responses, SnRK1 is involved in controlling the developmental plasticity and resilience under diverse environmental conditions in plants. In this review, through mining and analyzing the interactome and phosphoproteome data of SnRK1, we are highlighting its role in fundamental cellular processes such as gene regulation, protein synthesis, primary metabolism, protein trafficking, nutrient homeostasis, and autophagy. Along with the well-characterized molecular interaction in SnRK1 signaling, our analysis highlights several unchartered regions of SnRK1 signaling in plants such as its possible communication with chromatin remodelers, histone modifiers, and inositol phosphate signaling. We also discuss potential reciprocal interactions of SnRK1 signaling with other signaling pathways and cellular processes, which could be involved in maintaining flexibility and homeostasis under different environmental conditions. Overall, this review provides a comprehensive overview of the SnRK1 signaling network in plants and suggests many novel directions for future research.


2019 ◽  
Vol 7 (1) ◽  
Author(s):  
Natalie V. Klinard ◽  
Edmund A. Halfyard ◽  
Jordan K. Matley ◽  
Aaron T. Fisk ◽  
Timothy B. Johnson

Abstract Background Acoustic telemetry is an increasingly common method used to address ecological questions about the movement, behaviour, and survival of freshwater and marine organisms. The variable performance of acoustic telemetry equipment and ability of receivers to detect signals from transmitters have been well studied in marine and coral reef environments to inform study design and improve data interpretation. Despite the growing use of acoustic telemetry in large, deep, freshwater systems, detection efficiency and range, particularly in relation to environmental variation, are poorly understood. We used an array of 90 69-kHz acoustic receivers and 8 sentinel range transmitters of varying power output deployed at different depths and locations approximately 100–9500 m apart for 215 days to evaluate how the detection efficiency of acoustic receivers varied spatially and temporally in relation to environmental conditions. Results The maximum distance that tags were detected ranged from 5.9 to 9.3 km. Shallow tags consistently had lower detection efficiency than deep tags of the same power output and detection efficiency declined through the winter months (December–February) of the study. In addition to the distance between tag and receiver, thermocline strength, surface water velocity, ice thickness, water temperature, depth range between tag and receiver, and number of fish detections contributed to explaining variation in detection efficiency throughout the study period. Furthermore, the most significant models incorporated interactions between several environmental variables and tag–receiver distance, demonstrating the complex temporal and spatial relationships that exist in heterogeneous environments. Conclusions Relying on individual environmental variables in isolation to interpret receiver performance, and thus animal behaviour, may be erroneous when detection efficiency varies across distances, depths, or tag types. As acoustic telemetry becomes more widely used to study ecology and inform management, it is crucial to understand its limitations in heterogeneous environments, such as freshwater lakes, to improve the quality and interpretation of data. We recommend that in situ range testing and retrospective analysis of detection efficiency be incorporated into study design for telemetry projects. Furthermore, we caution against oversimplifying the dynamic relationship between detection efficiency and environmental conditions for the sake of producing a correction that can be applied directly to detection data of tagged animals when the intended correction may not be justified.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Xue Bian ◽  
Angela Pinilla ◽  
Tom Chandler ◽  
Richard Peters

AbstractHabitat-specific characteristics can affect signal transmission such that different habitats dictate the optimal signal. One way to examine how the environment influences signals is by comparing changes in signal effectiveness in different habitats. Examinations of signal effectiveness between different habitats has helped to explain signal divergence/convergence between populations and species using acoustic and colour signals. Although previous research has provided evidence for local adaptations and signal divergence in many species of lizards, comparative studies in movement-based signals are rare due to technical difficulties in quantifying movements in nature and ethical restrictions in translocating animals between habitats. We demonstrate herein that these issues can be addressed using 3D animations, and compared the relative performance of the displays of four Australian lizard species in the habitats of each species under varying environmental conditions. Our simulations show that habitats differentially affect signal performance, and an interaction between display and habitat structure. Interestingly, our results are consistent with the hypothesis that the signal adapted to the noisier environment does not show an advantage in signal effectiveness, but the noisy habitat was detrimental to the performance of all displays. Our study is one of the first studies for movement-based signals that directly compares signal performance in multiple habitats, and our approach has laid the foundation for future investigations in motion ecology that have been intractable to conventional research methods.


2018 ◽  
Vol 84 (18) ◽  
Author(s):  
Qi-Peng He ◽  
Shuai Zhao ◽  
Jiu-Xiang Wang ◽  
Cheng-Xi Li ◽  
Yu-Si Yan ◽  
...  

ABSTRACTSoil fungi produce a wide range of chemical compounds and enzymes with potential for applications in medicine and biotechnology. Cellular processes in soil fungi are highly dependent on the regulation under environmentally induced stress, but most of the underlying mechanisms remain unclear. Previous work identified a key GATA-type transcription factor,Penicillium oxalicumNsdD (PoxNsdD; also called POX08415), that regulates the expression of cellulase and xylanase genes inP. oxalicum. PoxNsdD shares 57 to 64% identity with the key activator NsdD, involved in asexual development inAspergillus. In the present study, the regulatory roles of PoxNsdD inP. oxalicumwere further explored. Comparative transcriptomic profiling revealed that PoxNsdD regulates major genes involved in starch, cellulose, and hemicellulose degradation, as well as conidiation and pigment biosynthesis. Subsequent experiments confirmed that a ΔPoxNsdDstrain lost 43.9 to 78.8% of starch-digesting enzyme activity when grown on soluble corn starch, and it produced 54.9 to 146.0% more conidia than the ΔPoxKu70parental strain. During cultivation, ΔPoxNsdDcultures changed color, from pale orange to brick red, while the ΔPoxKu70cultures remained bluish white. Real-time quantitative reverse transcription-PCR showed thatPoxNsdDdynamically regulated the expression of a glucoamylase gene (POX01356/Amy15A), an α-amylase gene (POX09352/Amy13A), and a regulatory gene (POX03890/amyR), as well as a polyketide synthase gene (POX01430/alb1/wA) for yellow pigment biosynthesis and a conidiation-regulated gene (POX06534/brlA). Moreover,in vitrobinding experiments showed that PoxNsdD bound the promoter regions of the above-described genes. This work provides novel insights into the regulatory mechanisms of fungal cellular processes and may assist in genetic engineering ofP.oxalicumfor potential industrial and medical applications.IMPORTANCEMost filamentous fungi produce a vast number of extracellular enzymes that are used commercially for biorefineries of plant biomass to produce biofuels and value-added chemicals, which might promote the transition to a more environmentally friendly economy. The expression of these extracellular enzyme genes is tightly controlled at the transcriptional level, which limits their yields. Hitherto our understanding of the regulation of expression of plant biomass-degrading enzyme genes in filamentous fungi has been rather limited. In the present study, regulatory roles of a key regulator, PoxNsdD, were further explored in the soil fungusPenicillium oxalicum, contributing to the understanding of gene regulation in filamentous fungi and revealing the biotechnological potential ofP.oxalicumvia genetic engineering.


2004 ◽  
Vol 1 (1) ◽  
pp. 393-412 ◽  
Author(s):  
F. Keppler ◽  
R. M. Kalin ◽  
D. B. Harper ◽  
W. C. McRoberts ◽  
J. T. G. Hamilton

Abstract. We report that the most abundant C1 units of terrestrial plants, the methoxyl groups of pectin and lignin, have a unique carbon isotope signature exceptionally depleted in 13C. Plant-derived C1 volatile organic compounds (VOCs) are also anomalously depleted in 13C compared with Cn+1 VOCs. The results confirm that the plant methoxyl pool is the predominant source of biospheric C1 compounds of plant origin such as methanol, chloromethane and bromomethane. Furthermore this pool, comprising ca. 2.5% of carbon in plant biomass, represents an important substrate for methanogenesis and could be a significant source of isotopically light methane entering the atmosphere. Our findings have significant implications for the use of carbon isotope ratios in elucidation of global carbon cycling. Moreover methoxyl groups could act as markers for biological activity in organic matter of terrestrial and extraterrestrial origin.


2017 ◽  
Author(s):  
Tracy Elsey-Quirk ◽  
Viktoria Unger

Abstract. Environmental conditions have a strong influence on rates plant productivity and decomposition. In salt marshes, hydrology and salinity are important regulators of plant and soil processes, which, in turn, can influence the rate at which marsh ecosystems accumulate C and adjust to sea-level rise. For this study, we examined the influence of multivariate environmental conditions on belowground ingrowth (roots + rhizomes), decomposition and biomass in marshes dominated by Spartina alterniflora across two estuaries and a range of geomorphic settings. Secondly, we examined the influence of belowground plant biomass to soil C density, and C (labile and refractory) accumulation and accretion rates. Study locations occupied a full range of tidal elevations from below mean low water to above mean high water. Salinities ranged from 7–40, and soil properties also varied across marshes. While many of the environmental parameters were correlated across marshes, belowground ingrowth of S. alterniflora was negatively influenced by mean low water height, such that root growth increased with more drainage. Belowground decay rate increased with increasing salinity, but ultimately the percent of mass remaining was similar across marshes, averaging 59 ± 1 %. Above- and belowground biomass dynamics were estuary-dependent. In the coastal lagoon estuary, less flooding and a higher sedimentation rate favored above-and belowground biomass, which, in turn, increased soil C accumulation and accretion rates. Biomass dynamics in the coastal plain estuary, for the most part, were unrelated to environmental predictor variables, and had little influence on the accumulation of soil C or accretion rate. These findings indicate that mineral sedimentation is of utmost importance for promoting belowground biomass and soil C accumulation in sediment-limited systems while in minerogenic systems, belowground biomass may not scale with C accumulation and accretion, which may be influenced more by smaller submillimetre-sized C particles.


PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9586
Author(s):  
László Fülöp ◽  
János Ecker

Recycling biomass is indispensable these days not only because fossil energy sources are gradually depleted, but also because pollution of the environment, caused by the increasing use of energy, must be reduced. This article intends to overview the results of plant biomass processing methods that are currently in use. Our aim was also to review published methods that are not currently in use. It is intended to explore the possibilities of new methods and enzymes to be used in biomass recycling. The results of this overview are perplexing in almost every area. Advances have been made in the pre-treatment of biomass and in the diversity and applications of the enzymes utilized. Based on molecular modeling, very little progress has been made in the modification of existing enzymes for altered function and adaptation for the environmental conditions during the processing of biomass. There are hardly any publications in which molecular modeling techniques are used to improve enzyme function and to adapt enzymes to various environmental conditions. Our view is that using modern computational, biochemical, and biotechnological methods would enable the purposeful design of enzymes that are more efficient and suitable for biomass processing.


2011 ◽  
Vol 59 (3) ◽  
pp. 217-222
Author(s):  
J. Pintér ◽  
I. Pók ◽  
T. Janda ◽  
Z. Szigeti ◽  
C. Marton

Solar UV-B radiation is generally regarded as an environmental stress factor, causing harm to living organisms by damaging DNA, proteins, lipids and membranes. Increased UV-B radiation may affect plant life directly or indirectly, having an influence on photosynthesis and plant biomass. In many plants, including maize (which is one of the most important crops in the world), exposure to increased UV-B radiation causes the induction of UV-B absorbing compounds (e.g. flavonoids), which act as UV-B screens and reduce the dangerous levels and effects of this radiation in plant tissues and cells.This study aimed to reveal how Martonvásár maize inbred lines (bred under Central European environmental conditions) respond to increased UV-B radiation.


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