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The genus Phragmites includes several species, of which only Phragmites australis has a worldwide distribution. It has been several decades since the last formal taxonomic examination of the genus and a number of recent genetic studies have revealed novel diversity and unique lineages within the genus. In my initial work on genetic variation in Phragmites (Saltonstall in Proc Nat Acad Sci 99:2445–2449, 2002 ), I came up with a naming scheme for identifying chloroplast DNA haplotypes which combined unique sequences at two loci, designated by numbers, to form haplotypes, designated by letters. Here I describe this naming system in more detail, explain how it has evolved over time as more genetic data has become available, provide a summary of all haplotypes currently available on GenBank, and address some common misunderstandings about how the haplotypes are named.

Cryptic invasions are a largely unrecognized type of biological invasion that lead to underestimation of the total numbers and impacts of invaders because of the difficulty in detecting them. The distribution and abundance of Phragmites australis in North America has increased dramatically over the past 150 years. This research tests the hypothesis that a non-native strain of Phragmites is responsible for the observed spread. Two noncoding chloroplast DNA regions were sequenced for samples collected worldwide, throughout the range of Phragmites. Modern North American populations were compared with historical ones from herbarium collections. Results indicate that an introduction has occurred, and the introduced type has displaced native types as well as expanded to regions previously not known to have Phragmites. Native types apparently have disappeared from New England and, while still present, may be threatened in other parts of North America.

Phosphorus (P) is an essential nutrient that is often in limited supply, with P availability constraining biomass production in many terrestrial ecosystems. Despite decades of work on plant responses to P deficiency and the importance of soil microbes to terrestrial ecosystem processes, how soil microbes respond to, and cope with, P deficiencies remains poorly understood. We studied 583 soils from two independent sample sets that each span broad natural gradients in extractable soil P and collectively represent diverse biomes, including tropical forests, temperate grasslands, and arid shrublands. Phosphorus (P) is an essential nutrient that is often in limited supply, with P availability constraining biomass production in many terrestrial ecosystems. Despite decades of work on plant responses to P deficiency and the importance of soil microbes to terrestrial ecosystem processes, how soil microbes respond to, and cope with, P deficiencies remains poorly understood. We studied 583 soils from two independent sample sets that each span broad natural gradients in extractable soil P and collectively represent diverse biomes, including tropical forests, temperate grasslands, and arid shrublands. We paired marker gene and shotgun metagenomic analyses to determine how soil bacterial and archaeal communities respond to differences in soil P availability and to detect corresponding shifts in functional attributes. We identified microbial taxa that are consistently responsive to extractable soil P, with those taxa found in low P soils being more likely to have traits typical of oligotrophic life history strategies. Using environmental niche modeling of genes and gene pathways, we found an enriched abundance of key genes in low P soils linked to the carbon-phosphorus (C-P) lyase and phosphonotase degradation pathways, along with key components of the high-affinity phosphate-specific transporter (Pst) and phosphate regulon (Pho) systems. Taken together, these analyses suggest that catabolism of phosphonates is an important strategy used by bacteria to scavenge phosphate in P-limited soils. Surprisingly, these same pathways are important for bacterial growth in P-limited marine waters, highlighting the shared metabolic strategies used by both terrestrial and marine microbes to cope with P limitation.

Land use is known to affect water quality yet the impact it has on aquatic microbial communities in tropical systems is poorly understood. We used 16S metabarcoding to assess the impact of land use on bacterial communities in the water column of four streams in central Panama. Each stream was influenced by a common Neotropical land use: mature forest, secondary forest, silvopasture and traditional cattle pasture. Bacterial community diversity and composition were significantly influenced by nearby land uses. Streams bordered by forests had higher phylogenetic diversity (Faith’s PD) and similar community structure (based on weighted UniFrac distance), whereas the stream surrounded by traditional cattle pasture had lower diversity and unique bacterial communities. The silvopasture stream showed strong seasonal shifts, with communities similar to forested catchments during the wet seasons and cattle pasture during dry seasons. We demonstrate that natural forest regrowth and targeted management, such as maintaining and restoring riparian corridors, benefit stream-water microbiomes in tropical landscapes and can provide a rapid and efficient approach to balancing agricultural activities and water quality protection.

Legume trees form an abundant and functionally important component of tropical forests worldwide with N₂-fixing symbioses linked to enhanced growth and recruitment in early secondary succession. However, it remains unclear how N₂-fixers meet the high demands for inorganic nutrients imposed by rapid biomass accumulation on nutrient-poor tropical soils. Here, we show that N₂-fixing trees in secondary Neotropical forests triggered twofold higher in situ weathering of fresh primary silicates compared to non-N₂–fixing trees and induced locally enhanced nutrient cycling by the soil microbiome community. Shotgun metagenomic data from weathered minerals support the role of enhanced nitrogen and carbon cycling in increasing acidity and weathering. Metagenomic and marker gene analyses further revealed increased microbial potential beneath N₂-fixers for anaerobic iron reduction, a process regulating the pool of phosphorus bound to iron-bearing soil minerals. We find that the Fe(III)-reducing gene pool in soil is dominated by acidophilic Acidobacteria, including a highly abundant genus of previously undescribed bacteria, Candidatus Acidoferrum, genus novus. The resulting dependence of the Fe-cycling gene pool to pH determines the high iron-reducing potential encoded in the metagenome of the more acidic soils of N₂-fixers and their nonfixing neighbors. We infer that by promoting the activities of a specialized local microbiome through changes in soil pH and C:N ratios, N₂-fixing trees can influence the wider biogeochemical functioning of tropical forest ecosystems in a manner that enhances their ability to assimilate and store atmospheric carbon.

While hybridization between Native and Introduced Phragmites australis has not been documented across much of North America, it poses an ongoing threat to Native P. australis across its range. This is especially true for native populations in the biologically rich, but sparsely distributed wetlands of the southwest United States, which are among the most imperiled systems in North America. We identified multiple Hybrid P. australis stands in the Las Vegas Wash watershed, NV, a key regional link to the Colorado River basin. Rapid urbanization in this watershed has caused striking changes in water and nutrient inputs and the distribution of wetland habitats has also changed, with urban wetlands expanding but an overall reduction in wetland habitats regionally. Native P. australis has likely been present in the Wash wetland community in low abundance for thousands of years, but today Hybrid and Native plants dominate the shoreline along much of the Wash. In contrast, Introduced P. australis is rare, suggesting that opportunities for novel hybridization events remain uncommon. Hybrid crosses derived from both the native and introduced maternal lineages are widespread, although the conditions that precluded their establishment are unknown and we did not find evidence for backcrossing. Spread of Hybrid plants is likely associated with flooding events as well as restoration activities, including revegetation efforts and construction for erosion control, that have redistributed sediments containing P. australis rhizomes. Downstream escape of Hybrid plants to Lake Mead and wetlands throughout the lower Colorado River basin is of management concern as these Hybrids appear vigorous and could spread rapidly.

Polyploidy may contribute to invasive ability as it can lead to high survival and fitness during establishment and enhance the processes of adaptation to novel environments by increasing genetic diversity in invading propagules. Many grasses are polyploid and many are aggressive invaders, making them persistent problems in disturbed environments worldwide. Today, vast areas of central Panama are dominated by Saccharum spontaneum, a perennial grass that originates from Asia. While widely regarded as invasive, it is not known when or how it arrived in Panama. We explore hypotheses regarding the timing and origins of this invasion through literature review and comparisons of genetic diversity in Panama with accessions from available sugarcane germplasm collections, highlighting historical accessions that were likely brought to Panama in 1939 as part of a USDA sugarcane germplasm collection. Samples were haplotyped at two chloroplast loci and genotyped using eight microsatellite markers. All sequenced individuals from Panama belong to a single chloroplast lineage which is common worldwide and was common in the Historic germplasm collection. Although genotypic diversity was extremely high in all samples due to high ploidy, samples from Panama had reduced diversity and clustered with several accessions in the Historic collection which had the same haplotype and high ploidy levels. Our results suggest that accidental escape from the historical sugarcane germplasm collection is the likely origin of the S. spontaneum invasion in Panama. Intraspecific hybridization among several historical accessions and pre-adaptation to local conditions may have facilitated its rapid spread and persistence. We discuss the implications of our findings for biosecurity of germplasm collections.

The environmental and social impacts of Phragmites australis invasion have been extensively studied in the eastern United States. In the West where the invasion is relatively recent, a lack of information on distributions and spread has limited our ability to manage invasive populations or assess whether native populations will experience a decline similar to that in the East. Between 2006 and 2015, we evaluated the genetic status, distribution, and soil properties (pH, electrical conductivity, and soil texture) of Phragmites stands in wetlands and riparian systems throughout the Southwest. Native (subspecies americanus ), Introduced (haplotype M), and Gulf Coast (subspecies berlandieri ) Phragmites lineages were identified in the survey region, as well as watershed-scale hybridization between the Native and Introduced lineages in southern Nevada. Two Asian haplotypes (P and Q) that were previously not known to occur in North America were found in California. The Native lineage was the most frequent and widespread across the region, with four cpDNA haplotypes (A, B, H, and AR) occurring at low densities in all wetland types. Most Introduced Phragmites stands were in or near major urban centers and associated with anthropogenic disturbance in wetlands and rivers, and we document their spread in the region, which is likely facilitated by transportation and urban development. Soil pH of Native and hybrid stands was higher (averaging 8.3 and 8.6, respectively) than Introduced stands (pH of 7.5) and was the only soil property that differed among lineages. Continued monitoring of all Phragmites lineages in the Southwest will aid in assessing the conservation status of Native populations and developing management priorities for non-native stands.

The common reed, genus Phragmites (Poaceae), is possibly the most widely distributed and well-studied plant in the world. It is found throughout temperate parts of the world and, while rarer in the tropics, generally dominates plant communities where it occurs, forming a characteristic tall-grass community in wetlands worldwide (Fig. 1). Phragmites has positive attributes as an ecosystem engineer and provides essential ecological and economic services, such as wildlife habitat, erosion control, improvement of water quality, and biomass production. However, Phragmites can also be an aggressive invader, particularly in North America where introductions of non-native Phragmites australis lineages have overtaken native communities (which sometimes include nativeP. australis subsp. americanus) and become dominant in wetlands across the continent.

Here, we assess the potential of airborne eDNA (airDNA) metabarcoding to characterize arthropod and vertebrate assemblages in a tropical forest. We deployed 28 high-flow air samplers across a 1.5 km 2 area on Barro Colorado Island, Panama, over two consecutive 24-hour periods and sequenced captured DNA using general eukaryotic and vertebrate-specific metabarcoding primers. AirDNA sampling detected 1293 arthropod operational taxonomic units (OTUs) with a COI primer set alongside 157 vertebrate OTUs representing birds, mammals, reptiles, amphibians, and fish with a 12S rRNA primer set. Arthropod richness was comparable to that quantified locally with light and Malaise trap surveys, while vertebrate richness exceeded that typically observed with conventional techniques. 76% of the arthropod OTU richness was assigned to Cecidomyiidae species. The level of field and lab effort employed in this study captured approximately 84% of the asymptotic richness for arthropods and 76% for vertebrates, implying that relatively little additional richness would have been quantified with additional effort within the same domain of sampling. Observed and asymptotic richness increased with the number of sites, the number of days a site was sampled, and the number of PCR replicates run per sample, highlighting the need to consider effort for future applications of airDNA to compare richness across systems. These results demonstrate that airDNA metabarcoding can efficiently and non-invasively profile high-diversity tropical terrestrial faunal assemblages.