Halophytes

Introduction

Over a century ago, halophytes were defined simply but usefully as species adapted to perpetually saline conditions. These occur naturally throughout the terrestrial earth. Sometimes, they are only transient, as following coastal flooding. In other cases, they are essentially perpetual, as in salt marshes or salt deserts. For the most part, the “salt” in “saline” is sodium chloride. Many soils, however, are affected by sodium carbonates or bicarbonates. Plants endemic to these “sodic” conditions may or may not also be able to grow in saline condition. Some, for example rice, may be much more adapted to sodic soils than saline ones.

More recently, for purposes of physiological and molecular studies, more precise operational definitions have been useful, i.e. as plants capable of completing their life cycles on salt levels ranging from ca. 80 to 300 mM NaCl, depending on the author. There is, however, no consensus regarding other nutrient levels or ratios in such studies. Most studies have been based on plants growing under eutrophic conditions, with high N, P and micronutrients, and Ca:Mg ratios of ca. 5:1. The most common term used to describe these is “Hoagland’s”.  Fewer studies have been based on sea water dilutions (very low N and P, and Ca:Mg ratios of 1:5).

Overall estimates of halophyte numbers now range from ~350 to 2600 species.  They are, however, not an evolutionarily coherent group. Halophytes occur in 37 of the 65 orders of plants. 1 No families are strictly halophytic although some have disproportionately high numbers (e.g. the Chenopodiaceae, now included in the Amaranthaceae). Both halophytes and non-halophytes frequently co-occur in the same genus, e.g. in Aster, Glycine, Plantago, Solanum and Oryza.

Historically, the effort to distinguish halophytes from “most” plants (i.e. the other 350,000 species of angiosperms) has been phrased in terms of “salt tolerance”, although halophytes can actually seem to be simply “salt indifferent”. While this approach of comparison and distinction can be continued indefinitely, it doesn’t seem to be leading to either great ecological understanding or to solutions to salinity related problems. This will be dealt with more in the last section.

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Evolution

How do halophytes evolve?

Large, unpredictable disruptions such as glaciers and volcanic eruptions, by creating severe habitat disequilibria, serve as the critical drivers in the evolution of halophytes and of edaphic endemics in general. 2 The severity of stress that follows disruption, particularly in contrast to neighboring habitats, the extent of the area affected, and proximity to existing similarly stressed sites determines the distinctiveness of the plant community that follows. The severity of the stress, for example, determines the number of marginally tolerant individuals suitable for colonizing the disturbed areas, while the other two factors determine the potential for migration of species among sites. Stress tolerant species colonizing ecological islands do not generally arise de novo. Rather, the founding individuals must be pre-adapted to the stresses, having previously evolved these capacities fortuitously in non-stressful habitats.

Following successful colonization, stabilization of the colonizers and their subsequent evolution as species involves both phenological and genomic changes. Both, critically, prevent – or at least greatly reduce – back-crossing with the original, unfit, progenitors; i.e. they lead to reproductive isolation.

L. maritima (yellow) and Romanzoffia tracyi (white) off the California coast. Photo courtesy of GD Carr.

The divergence of the halophyte, Lasthenia maritima (Asteraceae)from its progenitor, L. minor exemplifies the speed with which this can occur. 3 With the last retreat of the North American glaciers 10,000 to 15,000 years ago and concomitant rising sea levels, L. maritima evolved from a pre-adapted population of L. minor that was left stranded on guano encrusted and salt sprayed islands off the coast of California.

Clearly, what can evolve in a newly developing habitat depends on what is already present in the vicinity. This goes a long way to explaining the polyphyletic distributions of halophytes: orders, families or genera not present at such targets of opportunity do not include halophytes.

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New models

New experimental models for the evolution of halophytes

There are numerous established and potential model species having populations which differ significantly in their ability to colonize and survive in saline conditions. These may well prove useful in clarifying the development of halophily and the evolution of halophytes. Indeed, even Arabidopsis thaliana, across its wide distribution, may well have sufficient genetic variability that localized genotypes pre-adapted to salinity and other stresses already exist.4

Atriplex canescens, for example, occurs in populations with different ploidy levels and extremely different levels of sodium accumulation even over small geographic areas.5 Alternately, Lasthenia californica6occurs as at least two different races, one restricted to wet sites with high levels of Na+ and Mg2+ salts, and another which occurs at sites with much lower salinity, but also much less water. Under controlled conditions, plants of the first race accumulated 20-fold more Na+ than the second. L. maritima (noted earlier) originated only ca. 15,000 – 10,000 years ago and has its progenitor living nearby.

Helianthus paradoxus at the Bitter Lake NWR, Texas. Photo courtesy of Paul Tashjian.

Or, consider the case of Helianthus paradoxus (Asteraceae), a halophyte restricted to a few salt marshes in Texas and New Mexico (USA).7 This is one of three stabilized diploid hybrids of the less stress tolerant and more widespread H. annuus and H. petiolaris. In diploid hybrid speciation, expansion in a new environment is associated with rapid chromosomal re-patterning concomitant with niche separation. It is an interesting potential model because it has also been largely re-created artificially.8

Beyond these, any number of potential models is conceivable, but because of the time and money involved, it would be highly desirable for more than one lab to be interested in the project and for there to be some rationale more than mere intellectual curiosity, e.g. as a bona fide attempt to address some aspect of food security. Then, a program might use selection on saline soil to create a new halophyte exploiting adaptations already present in the global population. Progress could be monitored by resequencing the genome and transcriptome as well as by monitoring phenotypic changes. Indeed, these two approaches could be combined, selecting for ‘agronomic traits’ at high salinity.

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Genomics/evolution

Genomics and the evolution of halophytes 2

The pre-adaptation of a mesophyte to salt stress – the first requirement to evolution of a halophyte – requires a set of “starter” genes. Conversion to halophytism also requires post-colonization changes at the genome level. The archetypal pre-angiosperm ancestral genome likely had ca.12000 protein-coding genes. Around 320 MYA, there was a genome triplication contemporaneous with the origin of angiosperms, and at 190 MYA, a duplication. Both events are reflected in most of today’s angiosperm genomes. Even taking into account subsequent general and lineage-specific gene loss, the history of angiosperms provides a rich source of genes and their variants to serve as the starter set.

Genome duplications were, of course, not limited to these two events, and hybridization and autopolyploidy continue to occur. All these are thought to confer increased chances of survival in new or novel habitats.This may have been critical, for example, at the KT boundary 66 MYA which cleared many niches and opened many new ones. It has been postulated that the persistence and subsequent expansion of angiosperms across the boundary was associated with a large number of independent genome duplication events.

Not all halophytes are polyploids nor are all polyploids stress tolerant, reflecting gene loss that begins soon after duplication. In some cases, ploidy levels make little difference in salt tolerance, but in other cases, autopolyploids are more salt tolerant than diploids. The continued study of stable polyploids in relation to genome duplication events is clearly warranted. In this case, Atriplex canescens might be a good subject, having stable 2x, 4x, 6x, 8x,10x, 12x, 14x, and 20x chromosome races at least three of which (2x, 4x and 6x) may co-occur at individual sites.

Tandem duplications, gene translocations and transposable element (TE) insertions can also increase copy numbers of genes useful in stress tolerance. Their rate of occurrence may be accelerated by environmental challenges even in a few generations. The potential for deciphering and understanding their importance to halophyte evolution has been increased by the genome sequencing of Schrenkiella parvula and Eutrema salsugineum. Thus far, for example, because the two lineages diverged only about 12 MYA, macro-synteny still characterize the S. parvula and A. thaliana genomes, but with the S. parvula genome interrupted extensively by duplications, translocations and insertions absent in A. thaliana. The contributions of TEs and small RNAs to genome and transcriptome divergence has also been studied by comparing the chasmophyte, Arabidopsis lyrata, with A. thaliana.

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eHALOPH

eHALOPH – an Important halophyte resource

In the last several years, Flowers and co-workers 9 have undertaken to create and curate an electronic database of halophytes, called eHALOPH. This database dates to 1989 when James Aronson published a print list of 1,560 halophytes, ‘compiled for anyone growing or planning to grow halophytes’. Aronson’s list, included information on life form, plant type, distribution, maximum salinity tolerated, photosynthetic pathway and economic uses, and required that the presumed tolerance be manifested over a significant portion of the plant’s life cycle. Aronson’s original data have been supplemented – when possible – with links to literature on the “usual suspects”, i.e. antioxidants, secondary metabolites, compatible solutes, germination responses, molecular data, microbial interactions and mycorrhizal status. Geographical distribution information has been enriched in eHALOPH by providing distribution maps.

Although eHALOPH is already a very important and useful compendium, and its authors have invited users to help update it by supplying the information for their favorite species. At this point, they have listed more than 1500 species, and 265 entries have been fully curated. Their list of links to books and special journal issues devoted to halophytes is also a valuable contribution.

This database has numerous areas of application, including biosaline agriculture, phytoremediation and ecological rehabilitation of secondarily salinized areas, and ecological restoration of desert and coastal ecosystems that are naturally saline.

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Practical applications

Halophytes… where do we go from here?
As has been discussed elsewhere,2 a major question in need of attention now is – what experimental opportunities can be identified for better understanding the evolution of halophytes and glycophytes and for directing the evolution of salt tolerant crops? These are intimately linked. Several of these have already been presented, i.e. exploitation of recently evolved halophytes, of the genetic variation within Arabidopsis thaliana and other model plants, and of endemic halophytes. To these could be added the more intense investigation of minor crops to develop new crops for saline environments.

Understanding the mechanisms, at the genome level, by which halophytes evolve and by which domestication of crops proceeds, will facilitate the development of new crops. In the meantime, however, crops that can be grown on coastal or degraded soils should be considered the top priority in salinity related plant research. The combination of molecular and plant breeding approaches is critical here, as well as being quite do-able. Hancock10, for example noted that with modern breeding techniques, noted that the domestication process should require only 20–30 generations, a not inaccessible period.

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Acknowledgements

Acknowledgements –  This page was developed largely by John Cheeseman who gratefully acknowledges Tim Flowers (University of Sussex) for his assistance and valuable input.

Bibliography for the backstory

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Santos J, Al-Azzawi M, Aronson J, Flowers T. eHALOPH a Database of Salt-Tolerant Plants: Helping put Halophytes to Work. Plant Cell Physiol. 2016;57(1):e10. [PubMed]
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