Plantae

@misc{clements1920plant4,
    author = "Clements, F. E",
    title = "Plant Succession",
    year = "1920",
    howpublished = "An Analysis of the Development of Vegetation: Washington, D.C., Carnegie Institute, 388 p.; Publication No. 290",
    note = "talkorigins\_source = {true}; raw\_reference = {Clements, F. E., 1920, Plant Succession: An Analysis of the Development of Vegetation: Washington, D.C., Carnegie Institute, 388 p.; Publication No. 290.}"
}

@misc{beard1955the1,
    author = "Beard, J. S",
    title = "The classification of tropical American vegetation types",
    year = "1955",
    howpublished = "Ecology, v. 36, p. 89-100",
    note = "talkorigins\_source = {true}; raw\_reference = {Beard, J. S., 1955, The classification of tropical American vegetation types: Ecology, v. 36, p. 89-100.}"
}

@misc{billings1964plants2,
    author = "Billings, W. D",
    title = "Plants and the Ecosystem",
    year = "1964",
    howpublished = "Belmont, Ca., Wadsworth",
    note = "talkorigins\_source = {true}; raw\_reference = {Billings, W. D., 1964, Plants and the Ecosystem: Belmont, Ca., Wadsworth.}"
}

@misc{erhlich1964butterflies5,
    author = "Erhlich, P. R. and Raven, P. H",
    title = "Butterflies and plants",
    year = "1964",
    howpublished = "a study in coevolution: Evolution, v. 18, p. 586-608",
    note = "talkorigins\_source = {true}; raw\_reference = {Erhlich, P. R., and Raven, P. H., 1964, Butterflies and plants: a study in coevolution: Evolution, v. 18, p. 586-608.}"
}

@book{black1968soilplant3,
    author = "Black, C. A",
    title = "Soil-Plant Relationships [2nd ed.]",
    year = "1968",
    publisher = "New York, Wiley, 792 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Black, C. A., 1968, Soil-Plant Relationships [2nd ed.]: New York, Wiley, 792 p.}"
}

@inproceedings{whittaker1969evolution6,
    author = "Whittaker, R. H",
    title = "Evolution of diversity in plant communities",
    year = "1969",
    booktitle = "Brookhaven Symposium on Biology, v. 22, p. 178-196",
    note = "talkorigins\_source = {true}; raw\_reference = {Whittaker, R. H., 1969, Evolution of diversity in plant communities: Brookhaven Symposium on Biology, v. 22, p. 178-196.}"
}

@article{stjohn1975plantae,
    author = "St. John, Harold",
    title = "Plantae Hobdyanae Kauaienses II Hawaiian plant studies 45",
    year = "1975",
    journal = "The Botanical Magazine Tokyo",
    url = "https://doi.org/10.1007/bf02498881",
    doi = "10.1007/bf02498881",
    number = "1",
    pages = "59-64",
    volume = "88"
}

@incollection{crossref1992kingdom,
    title = "Kingdom Plantae (Plants)",
    year = "1992",
    booktitle = "Life in Amber",
    url = "https://doi.org/10.1515/9781503623545-012",
    doi = "10.1515/9781503623545-012",
    pages = "72-82"
}

@incollection{crossref2013plants,
    title = "Plants: Plantae",
    year = "2013",
    booktitle = "Encyclopedia of Metalloproteins",
    url = "https://doi.org/10.1007/978-1-4614-1533-6\_100989",
    doi = "10.1007/978-1-4614-1533-6\_100989",
    pages = "1694-1694"
}

Several medicinal plants are being used in Indian medicine systems since ancient times. However, in most cases, the specific molecules or the active ingredients responsible for the medicinal or therapeutic properties are not yet known. The objective of this study was to develop a computational protocol as well as a tool for generating novel potential drug candidates from the bioactive molecules of Indian medicinal and aromatic plants through the chemoinformatics approach. We employed chemoinformatics approaches to in-silico screened metabolites from 104 Indian medicinal and aromatic plants and designed novel drug-like bioactive molecules. For this purpose, 1665 ring-containing molecules were identified by text mining of literature related to the medicinal plant species, which were later used to extract 209 molecular scaffolds for building a focused virtual library. Virtual screening was performed with cluster analysis to predict drug-like and lead-like molecules from these plant molecules in the context of drug discovery.                 The predicted drug-like and lead-like molecules were evaluated using chemoinformatics approaches and statistical parameters, and only the most significant molecules were proposed as the candidate molecules to develop new drugs. A supra network of molecules and scaffolds identifying the relationships between the plant molecules and drugs was developed. Cluster analysis of virtual library molecules showed that the novel molecules had more pharmacophoric properties than toxicophoric and chemophoric properties. These predicted molecules need to be subjected to biological screening to identify potential molecules for drug discovery research. We also developed a Java-based open-source toolkit-cum-database called DoMINE (Database of Medicinally Important Natural products from plantaE) to advance the natural product-based drug discovery through chemoinformatics approaches. This study will be useful in developing new drug molecules from the known medicinal plant molecules. We hope that this work will encourage experimental organic chemists to synthesize these molecules based on the predicted values.

@phdthesis{karade2021design,
    author = "Karade, Divya",
    title = "Design of Novel Drug-like Molecules using Informatics Rich Secondary Metabolites Analysis of Indian Medicinal and Aromatic Plants",
    year = "2021",
    publisher = "Zenodo",
    abstract = "Several medicinal plants are being used in Indian medicine systems since ancient times. However, in most cases, the specific molecules or the active ingredients responsible for the medicinal or therapeutic properties are not yet known. The objective of this study was to develop a computational protocol as well as a tool for generating novel potential drug candidates from the bioactive molecules of Indian medicinal and aromatic plants through the chemoinformatics approach. We employed chemoinformatics approaches to in-silico screened metabolites from 104 Indian medicinal and aromatic plants and designed novel drug-like bioactive molecules. For this purpose, 1665 ring-containing molecules were identified by text mining of literature related to the medicinal plant species, which were later used to extract 209 molecular scaffolds for building a focused virtual library. Virtual screening was performed with cluster analysis to predict drug-like and lead-like molecules from these plant molecules in the context of drug discovery. The predicted drug-like and lead-like molecules were evaluated using chemoinformatics approaches and statistical parameters, and only the most significant molecules were proposed as the candidate molecules to develop new drugs. A supra network of molecules and scaffolds identifying the relationships between the plant molecules and drugs was developed. Cluster analysis of virtual library molecules showed that the novel molecules had more pharmacophoric properties than toxicophoric and chemophoric properties. These predicted molecules need to be subjected to biological screening to identify potential molecules for drug discovery research. We also developed a Java-based open-source toolkit-cum-database called DoMINE (Database of Medicinally Important Natural products from plantaE) to advance the natural product-based drug discovery through chemoinformatics approaches. This study will be useful in developing new drug molecules from the known medicinal plant molecules. We hope that this work will encourage experimental organic chemists to synthesize these molecules based on the predicted values.",
    url = "https://zenodo.org/doi/10.5281/zenodo.5637174",
    doi = "10.5281/zenodo.5637174"
}

When exposed to salinity, plants increase production of various organic osmolytes, termed "compatible solutes"(CS). Their role is often assumed to be osmotic, but the expense of producing high levels of endogenous CS (compared with taking up cheap inorganic ions from soil), casts doubt on this assumption. CS have a plethora of other putative means of alleviating stress, which have proved hard to disentangle and verify, due both to their overlapping effects and the overlap with other stress relieving mechanisms. This work aimed to quantify salt stress-induced changes in plant CS profiles and link them to adaptive responses to salinity in a range of 7 species contrasting in their salt tolerance, with different anatomical features (monocots vs dicots). Previous studies have been limited either by a narrow range of studied solute types or by a lack of quantification, thus we first developed a method using UHPLC and MS/MS to efficiently identify and quantify all of the organic solutes that responded to salt stress in the studied plant species. In all species, the overall amount of Na and K in leaves (especially in the youngest leaves) was constantly proportional to the sum of CS and Cl, prompting a new explanation for the involvement of CS in osmotic adjustment. According to this explanation, CS offset the toxic effects of inorganic solutes, raising their threshold of toxicity and allowing them to be used as osmolytes. This is not mutually exclusive with the conventional explanation for the use of CS in osmotic adjustment, which is that CS are used in the cytoplasm to balance the osmolarity of the vacuole (in which osmotic adjustment is achieved with inorganic ions). However, the levels of CS synthesised in response to salt treatment were often several times higher than needed for osmotic adjustment in the cytoplasm, suggesting that this was not their sole purpose. Further, the conventional explanation implies that the ratio of CS to inorganic ions should fall with salt treatment (as the vacuole expands and the cytosol contracts) and this was not so. In contrast to some prior reports, potassium maintained constant levels in young leaves and contributed little to osmotic adjustment, but its contribution increased as leaf age did. Salt tolerant plants were distinguished by segregation of Na between old and young leaves. This essential salt tolerance trait has been very under-reported. Comparisons of species showed that while Na exclusion from shoots was important, Na segregation between old and young leaves was more important. Salt tolerant plants were also distinguished by their ability to keep low levels of K in old leaves to spare K for young leaves and by their ability to increase the percentage of osmolarity accounted for by sucrose in the strongest salt treatments (although sucrose levels may fluctuate with lower salt treatments). In sensitive plants, the percentage of osmolarity accounted for by sucrose reached a clear maximum in the 50 or 100 mM salt treatment and fell in higher salt treatments. The ranking of species by total CS varied from one salt treatment to another, and a good correlation with salt tolerance was only achieved by using the maximum induced solute level of each species. Constitutive (control) levels did not relate to salt tolerance. Conversely, the major CS glycine betaine and proline correlated well with salt tolerance when control levels were used, implying that high constitutive levels of these solutes distinguish salt tolerant genotypes. Since some species emphasised glycine betaine and others emphasised proline, a more widely applicable correlation with salt tolerance was found by using the sum of glycine betaine and proline rather than either alone. CS often failed to correlate with salt tolerance when expressed as µmol/g of dry leaf weight; yet they correlated well when expressed as a percentage of osmolarity - which is rarely done. Fv/Fm did not correlate with salt tolerance unless measured on old leaves, which is of considerable practical importance for the use of this rapid screening tool. Several organic solutes that have rarely or never been linked to salt tolerance were found to correlate with salt tolerance in our study. These included malate, pipecolate, GBB (gamma-butyrobetaine), adenine and adenosine. Malate is probably not a driver of salt tolerance, but rather reflects the ability of a plant to protect malate-synthesising enzymes (with high CS levels and by excluding Na from cytoplasm). Pipecolate was uniquely correlated to the major CS of every species, suggesting that it either enhances the effects of these CS or stimulates their synthesis. The latter is likely, considering that studies of biotic stress have shown pipecolate to be essential to the role of salicylate. Pipecolate also correlated with adenosine and/or GABA in most species, hinting at influence over energy metabolism. GBB correlated negatively with glycine betaine, for which reason we tentatively suggest that in some niche it may fulfil a task otherwise filled by glycine betaine. GABA correlated with Na levels only in the species expected to have the highest energy demand for Na exclusion, which were also the only species in which adenine and adenosine correlated with Na. GABA also had notably frequent correlations with adenine and adenosine, all of which points to the importance of the GABA shunt in salinity. There was evidence that both malate synthesis and operation of PSII (quantified by Fv/Fm) were protected by inositol and sucrose, for which reason these solutes may be recommended for trials with exogenous use. GABA can also be recommended for trials with exogenous use, if feedstock for the GABA shunt would be helpful. Glycine betaine and proline were responsive to different stress levels (proline only responded to high stress, in which glycine betaine fell), suggesting that for exogenous treatments these solutes may be appropriate for different stress levels or may need to be used in specific ratios. In addition to the UHPLC work, we used salt treatment to manipulate endogenous CS levels and demonstrated a dose-dependent cross-tolerance in leaves later exposed to UV-B radiation (oxidative stress). This is the first in plantae evidence of a dose-dependent relationship between endogenous CS and oxidative stress tolerance, and these findings are helpful for understanding plant performance in real field situations, when they are often subjected to multiple stresses. The same methods of solute analysis were also applied to a waterlogging study of the same plant species. The dicots (all sensitive to waterlogging) suffered a fall in shoot water content while the grasses did not, pointing to different causes of stress. Thus, Fv/Fm correlated with tolerance in grasses but not dicots, while the reverse was true for shoot water content. Likewise organic solutes that correlated with tolerance in dicots were generally those that are known to relate to osmotic stress, whereas these did not correlate with tolerance in grasses. Those that correlated with tolerance in grasses correlated with dry matter accumulation rather than shoot water content. The solute with the strongest correlation with tolerance of grasses was choline, but only in young leaves. In old leaves of grasses choline did not correlate with tolerance but did correlate with shoot water content. GABA and pipecolate also correlated with tolerance in grasses. GABA also correlated with tolerance in dicots, correlating with growth rather shoot water content. Several solutes that did not correlate with tolerance were yet strongly responsive to waterlogging (malate, adenine, GBB, tyramine and inositol). Plausible physiological reasons for these responses and correlations are presented. Fv/Fm only correlated with tolerance of grasses when measured on the youngest leaf (and then did so very well). Fv/Fm is usually measured on mature leaves and gives poor correlations with waterlogging tolerance, so this finding potentially facilitates the use of Fv/Fm as a practical selection tool for plant breeders. Overall, this work brings a new understanding of the interaction between organic and inorganic osmolytes, suggests hitherto unknown physiological roles for several organic solutes in salinity stressed or waterlogged plants, and new insights into the roles of the major solutes glycine betaine, proline and GABA. From a practical perspective, this work presents a method of identifying and quantifying a wide range of organic solutes in plants, and methods of optimising correlations between organic solutes and salt tolerance. It presents solutes that are drivers or indicators of salt tolerance and waterlogging tolerance for the purposes of study, or plant selection and breeding. It reveals the importance of segregating both Na and K between old and young leaves as an essential salt tolerance trait, and shows that the use of Fv/Fm in plant breeding may be facilitated by using the appropriate leaf age group. Some solutes have emerged as potential exogenous treatments, as did evidence that the well-known treatments with glycine betaine and proline may be better used in specific ratios.

@phdthesis{puniranhartley2024understanding,
    author = "Puniran-Hartley, N",
    title = "Understanding the role of compatible solutes in adaptive responses of plants to salinity and waterlogging",
    year = "2024",
    publisher = "University of Tasmania",
    abstract = {When exposed to salinity, plants increase production of various organic osmolytes, termed "compatible solutes"(CS). Their role is often assumed to be osmotic, but the expense of producing high levels of endogenous CS (compared with taking up cheap inorganic ions from soil), casts doubt on this assumption. CS have a plethora of other putative means of alleviating stress, which have proved hard to disentangle and verify, due both to their overlapping effects and the overlap with other stress relieving mechanisms. This work aimed to quantify salt stress-induced changes in plant CS profiles and link them to adaptive responses to salinity in a range of 7 species contrasting in their salt tolerance, with different anatomical features (monocots vs dicots). Previous studies have been limited either by a narrow range of studied solute types or by a lack of quantification, thus we first developed a method using UHPLC and MS/MS to efficiently identify and quantify all of the organic solutes that responded to salt stress in the studied plant species. In all species, the overall amount of Na and K in leaves (especially in the youngest leaves) was constantly proportional to the sum of CS and Cl, prompting a new explanation for the involvement of CS in osmotic adjustment. According to this explanation, CS offset the toxic effects of inorganic solutes, raising their threshold of toxicity and allowing them to be used as osmolytes. This is not mutually exclusive with the conventional explanation for the use of CS in osmotic adjustment, which is that CS are used in the cytoplasm to balance the osmolarity of the vacuole (in which osmotic adjustment is achieved with inorganic ions). However, the levels of CS synthesised in response to salt treatment were often several times higher than needed for osmotic adjustment in the cytoplasm, suggesting that this was not their sole purpose. Further, the conventional explanation implies that the ratio of CS to inorganic ions should fall with salt treatment (as the vacuole expands and the cytosol contracts) and this was not so. In contrast to some prior reports, potassium maintained constant levels in young leaves and contributed little to osmotic adjustment, but its contribution increased as leaf age did. Salt tolerant plants were distinguished by segregation of Na between old and young leaves. This essential salt tolerance trait has been very under-reported. Comparisons of species showed that while Na exclusion from shoots was important, Na segregation between old and young leaves was more important. Salt tolerant plants were also distinguished by their ability to keep low levels of K in old leaves to spare K for young leaves and by their ability to increase the percentage of osmolarity accounted for by sucrose in the strongest salt treatments (although sucrose levels may fluctuate with lower salt treatments). In sensitive plants, the percentage of osmolarity accounted for by sucrose reached a clear maximum in the 50 or 100 mM salt treatment and fell in higher salt treatments. The ranking of species by total CS varied from one salt treatment to another, and a good correlation with salt tolerance was only achieved by using the maximum induced solute level of each species. Constitutive (control) levels did not relate to salt tolerance. Conversely, the major CS glycine betaine and proline correlated well with salt tolerance when control levels were used, implying that high constitutive levels of these solutes distinguish salt tolerant genotypes. Since some species emphasised glycine betaine and others emphasised proline, a more widely applicable correlation with salt tolerance was found by using the sum of glycine betaine and proline rather than either alone. CS often failed to correlate with salt tolerance when expressed as µmol/g of dry leaf weight; yet they correlated well when expressed as a percentage of osmolarity - which is rarely done. Fv/Fm did not correlate with salt tolerance unless measured on old leaves, which is of considerable practical importance for the use of this rapid screening tool. Several organic solutes that have rarely or never been linked to salt tolerance were found to correlate with salt tolerance in our study. These included malate, pipecolate, GBB (gamma-butyrobetaine), adenine and adenosine. Malate is probably not a driver of salt tolerance, but rather reflects the ability of a plant to protect malate-synthesising enzymes (with high CS levels and by excluding Na from cytoplasm). Pipecolate was uniquely correlated to the major CS of every species, suggesting that it either enhances the effects of these CS or stimulates their synthesis. The latter is likely, considering that studies of biotic stress have shown pipecolate to be essential to the role of salicylate. Pipecolate also correlated with adenosine and/or GABA in most species, hinting at influence over energy metabolism. GBB correlated negatively with glycine betaine, for which reason we tentatively suggest that in some niche it may fulfil a task otherwise filled by glycine betaine. GABA correlated with Na levels only in the species expected to have the highest energy demand for Na exclusion, which were also the only species in which adenine and adenosine correlated with Na. GABA also had notably frequent correlations with adenine and adenosine, all of which points to the importance of the GABA shunt in salinity. There was evidence that both malate synthesis and operation of PSII (quantified by Fv/Fm) were protected by inositol and sucrose, for which reason these solutes may be recommended for trials with exogenous use. GABA can also be recommended for trials with exogenous use, if feedstock for the GABA shunt would be helpful. Glycine betaine and proline were responsive to different stress levels (proline only responded to high stress, in which glycine betaine fell), suggesting that for exogenous treatments these solutes may be appropriate for different stress levels or may need to be used in specific ratios. In addition to the UHPLC work, we used salt treatment to manipulate endogenous CS levels and demonstrated a dose-dependent cross-tolerance in leaves later exposed to UV-B radiation (oxidative stress). This is the first in plantae evidence of a dose-dependent relationship between endogenous CS and oxidative stress tolerance, and these findings are helpful for understanding plant performance in real field situations, when they are often subjected to multiple stresses. The same methods of solute analysis were also applied to a waterlogging study of the same plant species. The dicots (all sensitive to waterlogging) suffered a fall in shoot water content while the grasses did not, pointing to different causes of stress. Thus, Fv/Fm correlated with tolerance in grasses but not dicots, while the reverse was true for shoot water content. Likewise organic solutes that correlated with tolerance in dicots were generally those that are known to relate to osmotic stress, whereas these did not correlate with tolerance in grasses. Those that correlated with tolerance in grasses correlated with dry matter accumulation rather than shoot water content. The solute with the strongest correlation with tolerance of grasses was choline, but only in young leaves. In old leaves of grasses choline did not correlate with tolerance but did correlate with shoot water content. GABA and pipecolate also correlated with tolerance in grasses. GABA also correlated with tolerance in dicots, correlating with growth rather shoot water content. Several solutes that did not correlate with tolerance were yet strongly responsive to waterlogging (malate, adenine, GBB, tyramine and inositol). Plausible physiological reasons for these responses and correlations are presented. Fv/Fm only correlated with tolerance of grasses when measured on the youngest leaf (and then did so very well). Fv/Fm is usually measured on mature leaves and gives poor correlations with waterlogging tolerance, so this finding potentially facilitates the use of Fv/Fm as a practical selection tool for plant breeders. Overall, this work brings a new understanding of the interaction between organic and inorganic osmolytes, suggests hitherto unknown physiological roles for several organic solutes in salinity stressed or waterlogged plants, and new insights into the roles of the major solutes glycine betaine, proline and GABA. From a practical perspective, this work presents a method of identifying and quantifying a wide range of organic solutes in plants, and methods of optimising correlations between organic solutes and salt tolerance. It presents solutes that are drivers or indicators of salt tolerance and waterlogging tolerance for the purposes of study, or plant selection and breeding. It reveals the importance of segregating both Na and K between old and young leaves as an essential salt tolerance trait, and shows that the use of Fv/Fm in plant breeding may be facilitated by using the appropriate leaf age group. Some solutes have emerged as potential exogenous treatments, as did evidence that the well-known treatments with glycine betaine and proline may be better used in specific ratios.},
    url = "https://figshare.utas.edu.au/articles/thesis/Understanding\_the\_role\_of\_compatible\_solutes\_in\_adaptive\_responses\_of\_plants\_to\_salinity\_and\_waterlogging/23246987/2",
    doi = "10.25959/23246987.v2"
}

Plants constantly experience partial hypoxia due to varying external oxygen availability and the existence of hypoxic niches, such as the shoot apical meristem, phloem or root nodules. Waterlogging experiments indicate that hypoxic stress at the root does not only lead to a local metabolic response, such as the accumulation of hypoxia-related metabolites, but also causes metabolic alterations in the normoxic shoot. Moreover, hypoxia-related metabolites are exported from the hypoxic root towards the normoxic shoot, where they can be recycled. Maintaining import of glycolytic substrates from the normoxic shoot into the hypoxic root is suggested to play a crucial role in managing hypoxic stress in waterlogged roots. These findings indicate that locally confined hypoxic stress induces systemic responses. The apparent metabolic interplay between hypoxic and normoxic tissue can facilitate the plant to endure differing oxygen availabilities between tissues and organs without active oxygen circulation. Here, we define this mechanism as 'metabolic snorkeling'. Beyond waterlogging, metabolic snorkeling might also occur between hypoxic niches and the adjacent normoxic tissue. In this review, the role of metabolic snorkeling in waterlogging-endurance and its applicability to hypoxic niches is described and discussed.

@article{doi101093jxberag184,
    author = "Herfurth, Freya and Fürtauer, Lisa and van Dongen, Joost T",
    title = "Metabolic Snorkeling - The Metabolic Interaction Between Plant Organs and Tissues with different Oxygen Availabilities.",
    year = "2026",
    journal = "Journal of experimental botany",
    abstract = "Plants constantly experience partial hypoxia due to varying external oxygen availability and the existence of hypoxic niches, such as the shoot apical meristem, phloem or root nodules. Waterlogging experiments indicate that hypoxic stress at the root does not only lead to a local metabolic response, such as the accumulation of hypoxia-related metabolites, but also causes metabolic alterations in the normoxic shoot. Moreover, hypoxia-related metabolites are exported from the hypoxic root towards the normoxic shoot, where they can be recycled. Maintaining import of glycolytic substrates from the normoxic shoot into the hypoxic root is suggested to play a crucial role in managing hypoxic stress in waterlogged roots. These findings indicate that locally confined hypoxic stress induces systemic responses. The apparent metabolic interplay between hypoxic and normoxic tissue can facilitate the plant to endure differing oxygen availabilities between tissues and organs without active oxygen circulation. Here, we define this mechanism as 'metabolic snorkeling'. Beyond waterlogging, metabolic snorkeling might also occur between hypoxic niches and the adjacent normoxic tissue. In this review, the role of metabolic snorkeling in waterlogging-endurance and its applicability to hypoxic niches is described and discussed.",
    url = "https://pubmed.ncbi.nlm.nih.gov/42068204/",
    doi = "10.1093/jxb/erag184",
    pmid = "42068204"
}

During plant development and in response to stress conditions, autophagy contributes to the intracellular degradation of cellular components and subsequent nutrient recycling. As this process is highly connected to the nutrient status of the plant, autophagy also contributes to the mobilisation of sulfur from source to sink tissues as well as the maintenance of primary sulfate assimilation. In turn, sulfur signals regulate autophagy, with sulfide (an intermediate of primary sulfate assimilation) exerting a repressive effect and sulfur deficiency having a stimulatory effect. In addition to a sulfur deficiency response in the plant resulting from low external sulfate availability, stresses such as metal exposure also perturb sulfur metabolism and can induce a 'functional sulfur deficiency' response through a surge in the production of thiol-rich metal chelators. As autophagy is increasingly linked to metal stress responses, this review proposes potential pathways through which metal-induced autophagy is linked to perturbations in sulfur metabolism, focusing on redox alterations and sucrose non-fermenting 1 (SNF1)-related kinase (SnRK)/target of rapamycin (TOR)-mediated nutrient signalling. Lastly, the connection between autophagy and sulfur status to plant stress tolerance is also discussed in terms of potential valorisation strategies to maximise plant growth on metal-contaminated soils.

@article{doi101093jxberag211,
    author = "Vanbuel, Isabeau and Hendrix, Sophie and Maes, Céleste and Vanbriel, Lara and Kunnen, Kris and Cuypers, Ann",
    title = "Many roads lead to autophagy: the connection between sulfur metabolism and autophagy during metal stress in plants.",
    year = "2026",
    journal = "Journal of experimental botany",
    abstract = "During plant development and in response to stress conditions, autophagy contributes to the intracellular degradation of cellular components and subsequent nutrient recycling. As this process is highly connected to the nutrient status of the plant, autophagy also contributes to the mobilisation of sulfur from source to sink tissues as well as the maintenance of primary sulfate assimilation. In turn, sulfur signals regulate autophagy, with sulfide (an intermediate of primary sulfate assimilation) exerting a repressive effect and sulfur deficiency having a stimulatory effect. In addition to a sulfur deficiency response in the plant resulting from low external sulfate availability, stresses such as metal exposure also perturb sulfur metabolism and can induce a 'functional sulfur deficiency' response through a surge in the production of thiol-rich metal chelators. As autophagy is increasingly linked to metal stress responses, this review proposes potential pathways through which metal-induced autophagy is linked to perturbations in sulfur metabolism, focusing on redox alterations and sucrose non-fermenting 1 (SNF1)-related kinase (SnRK)/target of rapamycin (TOR)-mediated nutrient signalling. Lastly, the connection between autophagy and sulfur status to plant stress tolerance is also discussed in terms of potential valorisation strategies to maximise plant growth on metal-contaminated soils.",
    url = "https://pubmed.ncbi.nlm.nih.gov/42068137/",
    doi = "10.1093/jxb/erag211",
    pmid = "42068137"
}

Understanding how plants influence each other's spatial distribution is pivotal not only for interpreting current communities, but also for anticipating their responses to global changes. The combination of high-resolution, multi-scale sampling and novel statistical frameworks now enables us to identify species aggregations and segregations within their local co-occurrences. By applying this approach to approximately 800 plant species and their communities across the French Alps, we discovered that local species associations are dependent on soil acidity and nitrogen rather than climate. By building a regional network from these associations, we identified a centralised core comprising a few dominant, stress-tolerant graminoids and shrubs with high leaf dry matter content and no unique functional roles. Our findings demonstrate that plant community assembly is less dependent on random co-occurrence and more dependent on segregation around a few dominant, stress-tolerant species, with soil conditions modulating the outcome of local associations.

@article{doi101111ele70393,
    author = "Rohr, Matthias and Wendling, Alexandre and Münkemüller, Tamara and Gravel, Dominique and Galiez, Clovis and Renaud, Julien and Consortium, Orchamp and Thuiller, Wilfried",
    title = "Beyond Co-Occurrence: Multi-Scale Evidence for Segregation-Dominated Plant Networks in the French Alps.",
    year = "2026",
    journal = "Ecology letters",
    abstract = "Understanding how plants influence each other's spatial distribution is pivotal not only for interpreting current communities, but also for anticipating their responses to global changes. The combination of high-resolution, multi-scale sampling and novel statistical frameworks now enables us to identify species aggregations and segregations within their local co-occurrences. By applying this approach to approximately 800 plant species and their communities across the French Alps, we discovered that local species associations are dependent on soil acidity and nitrogen rather than climate. By building a regional network from these associations, we identified a centralised core comprising a few dominant, stress-tolerant graminoids and shrubs with high leaf dry matter content and no unique functional roles. Our findings demonstrate that plant community assembly is less dependent on random co-occurrence and more dependent on segregation around a few dominant, stress-tolerant species, with soil conditions modulating the outcome of local associations.",
    url = "https://pubmed.ncbi.nlm.nih.gov/42068051/",
    doi = "10.1111/ele.70393",
    pmid = "42068051"
}

Visually cataloging and quantifying the natural world requires pushing the boundaries of both detailed visual classification and counting at scale. Despite significant progress, particularly in crowd and traffic analysis, the fine-grained, taxonomy-aware plant counting remains underexplored in vision. In contrast to crowds, plants exhibit nonrigid morphologies and physical appearance variations across growth stages and environments. To fill this gap, we present TPC-268, the first plant counting benchmark incorporating plant taxonomy. Our dataset couples instance-level point annotations with Linnaean labels (kingdom -> species) and organ categories, enabling hierarchical reasoning and species-aware evaluation. The dataset features 10,000 images with 678,050 point annotations, includes 268 countable plant categories over 242 plant species in Plantae and Fungi, and spans observation scales from canopy-level remote sensing imagery to tissue-level microscopy. We follow the problem setting of class-agnostic counting (CAC), provide taxonomy-consistent, scale-aware data splits, and benchmark state-of-the-art regression- and detection-based CAC approaches. By capturing the biodiversity, hierarchical structure, and multi-scale nature of botanical and mycological taxa, TPC-268 provides a biologically grounded testbed to advance fine-grained class-agnostic counting. Dataset and code are available at https://github.com/tiny-smart/TPC-268.

@misc{xu2026plant,
    author = "Xu, Jinyu and Hu, Tianqi and Hu, Xiaonan and Zhou, Letian and Cao, Songliang and Zhang, Meng and Lu, Hao",
    title = "Plant Taxonomy Meets Plant Counting: A Fine-Grained, Taxonomic Dataset for Counting Hundreds of Plant Species",
    year = "2026",
    publisher = "arXiv",
    abstract = "Visually cataloging and quantifying the natural world requires pushing the boundaries of both detailed visual classification and counting at scale. Despite significant progress, particularly in crowd and traffic analysis, the fine-grained, taxonomy-aware plant counting remains underexplored in vision. In contrast to crowds, plants exhibit nonrigid morphologies and physical appearance variations across growth stages and environments. To fill this gap, we present TPC-268, the first plant counting benchmark incorporating plant taxonomy. Our dataset couples instance-level point annotations with Linnaean labels (kingdom -\> species) and organ categories, enabling hierarchical reasoning and species-aware evaluation. The dataset features 10,000 images with 678,050 point annotations, includes 268 countable plant categories over 242 plant species in Plantae and Fungi, and spans observation scales from canopy-level remote sensing imagery to tissue-level microscopy. We follow the problem setting of class-agnostic counting (CAC), provide taxonomy-consistent, scale-aware data splits, and benchmark state-of-the-art regression- and detection-based CAC approaches. By capturing the biodiversity, hierarchical structure, and multi-scale nature of botanical and mycological taxa, TPC-268 provides a biologically grounded testbed to advance fine-grained class-agnostic counting. Dataset and code are available at https://github.com/tiny-smart/TPC-268.",
    url = "https://arxiv.org/abs/2603.21229",
    doi = "10.48550/arxiv.2603.21229"
}