WORKS CITED:
Ahmad, F., I. Ahmad, and M. S. Khan. 2008. Screening of free-living
rhizospheric bacteria for their multiple plant growth promoting
activities. Microbiological Research 163:173–181.
Albani Rocchetti, G., C. G. Armstrong, T. Abeli, S. Orsenigo, C. Jasper,
S. Joly, A. Bruneau, M. Zytaruk, and J. C. Vamosi. 2021. Reversing
extinction trends: New uses of (old) herbarium specimens to accelerate
conservation action on threatened species. New Phytologist 230:433–450.
Albani Rocchetti, G., A. Carta, A. Mondoni, S. Godefroid, C. C. Davis,
G. Caneva, M. A. Albrecht, K. Alvarado, R. Bijmoer, R. Borosova, C.
Bräuchler, E. Breman, M. Briggs, S. Buord, L. H. Cave, N. G. Da Silva,
A. H. Davey, R. M. Davies, J. B. Dickie, M. Fabillo, A. Fleischmann, A.
Franks, G. Hall, G. Kantvilas, C. Klak, U. Liu, L. Medina, L. G.
Reinhammar, R. J. Sebola, I. Schönberger, P. Sweeney, H. Voglmayr, A.
White, J. J. Wieringa, E. Zippel, and T. Abeli. 2022. Selecting the best
candidates for resurrecting extinct-in-the-wild plants from herbaria.
Nature Plants 8:1385–1393.
Ardley, J. K., M. A. Parker, S. E. De Meyer, R. D. Trengove, G. W.
O’Hara, W. G. Reeve, R. J. Yates, M. J. Dilworth, A. Willems, and J. G.
Howieson. 2012. Microvirga lupini sp. nov., Microvirga
lotononidis sp. nov. and Microvirga zambiensis sp. nov. are
alphaproteobacterial root-nodule bacteria that specifically nodulate and
fix nitrogen with geographically and taxonomically separate legume
hosts. International Journal of Systematic and Evolutionary Microbiology
62:2579–2588.
Ardley, J. K., W. G. Reeve, G. W. O’Hara, R. J. Yates, M. J. Dilworth,
and J. G. Howieson. 2013. Nodule morphology, symbiotic specificity and
association with unusual rhizobia are distinguishing features of the
genus Listia within the southern African Crotalarioid clade
Lotononis s.l. Annals of Botany 112:1–15.
Bai, Y., F. D’Aoust, D. L. Smith, and B. T. Driscoll. 2002. Isolation of
plant-growth-promoting Bacillus strains from soybean root
nodules. Canadian Journal of Microbiology 48:230–238.
Benito, P., P. Alonso-Vega, C. Aguado, R. Luján, Y. Anzai, A. M. Hirsch,
and M. E. Trujillo. 2017. Monitoring the colonization and infection of
legume nodules by Micromonospora in co-inoculation experiments
with rhizobia. Scientific Reports 7:11051.
Bieker, V. C., F. Sánchez Barreiro, J. A. Rasmussen, M. Brunier, N.
Wales, and M. D. Martin. 2020. Metagenomic analysis of historical
herbarium specimens reveals a postmortem microbial community. Molecular
Ecology Resources 20:1206–1219.
Breakwell, D., C. Woolverton, B. MacDonald, K. Smith, and R. Robison.
2007. Colony morphology protocol. American Society for Microbiology.
Burbano, H. A., and R. M. Gutaker. 2023. Ancient DNA genomics and the
renaissance of herbaria. Science 382:59–63.
Campos, P. E., C. Groot Crego, K. Boyer, M. Gaudeul, C. Baider, D.
Richard, O. Pruvost, P. Roumagnac, B. Szurek, N. Becker, L. Gagnevin,
and A. Rieux. 2021. First historical genome of a crop bacterial pathogen
from herbarium specimen: Insights into citrus canker emergence. PLOS
Pathogens 17:e1009714.
Campos, P. E., O. Pruvost, K. Boyer, F. Chiroleu, T. T. Cao, M. Gaudeul,
C. Baider, T. M. A. Utteridge, N. Becker, A. Rieux, and L. Gagnevin.
2023. Herbarium specimen sequencing allows precise dating ofXanthomonas citri pv. citri diversification history. Nature
Communications 14:4306.
Chinnaswamy, A., T. Coba de la Peña, A. Stoll, D. de la Peña Rojo, J.
Bravo, A. Rincón, M. m. Lucas, and J. j. Pueyo. 2018. A nodule
endophytic Bacillus megaterium strain isolated fromMedicago polymorpha enhances growth, promotes nodulation byEnsifer medicae and alleviates salt stress in alfalfa plants.
Annals of Applied Biology 172:295–308.
Cinátl, J. 1969. Inorganic-organic multimolecular complexes of salt
solutions, culture media and biological fluids and their possible
significance for the origin of life. Journal of Theoretical Biology
23:1–10.
Danneels, B., J. Viruel, K. Mcgrath, S. B. Janssens, N. Wales, P.
Wilkin, and A. Carlier. 2021. Patterns of transmission and horizontal
gene transfer in the Dioscorea sansibarensis leaf symbiosis
revealed by whole-genome sequencing. Current Biology 31:2666-2673.e4.
Daru, B. H., E. A. Bowman, D. H. Pfister, and A. E. Arnold. 2018. A
novel proof of concept for capturing the diversity of endophytic fungi
preserved in herbarium specimens. Philosophical Transactions of the
Royal Society B: Biological Sciences 374:20170395.
De Meyer, S. E., K. De Beuf, B. Vekeman, and A. Willems. 2015. A large
diversity of non-rhizobial endophytes found in legume root nodules in
Flanders (Belgium). Soil Biology and Biochemistry 83:1–11.
Elliott, G. N., W.-M. Chen, J.-H. Chou, H.-C. Wang, S.-Y. Sheu, L.
Perin, V. M. Reis, L. Moulin, M. F. Simon, C. Bontemps, J. M.
Sutherland, R. Bessi, S. M. De Faria, M. J. Trinick, A. R. Prescott, J.
I. Sprent, and E. K. James. 2007. Burkholderia phymatum is a
highly effective nitrogen-fixing symbiont of Mimosa spp. and
fixes nitrogen ex planta. New Phytologist 173:168–180.
Forrest, L. L., M. L. Hart, M. Hughes, H. P. Wilson, K.-F. Chung, Y.-H.
Tseng, and C. A. Kidner. 2019. The limits of hyb-seq for herbarium
specimens: Impact of preservation techniques. Frontiers in Ecology and
Evolution 7.
Fraile, A., F. Escriu, M. A. Aranda, J. M. Malpica, A. J. Gibbs, and F.
García-Arenal. 1997. A century of tobamovirus evolution in an Australian
population of Nicotiana glauca . Journal of Virology
71:8316–8320.
Friesen, M. L., S. S. Porter, S. C. Stark, E. J. von Wettberg, J. L.
Sachs, and E. Martinez-Romero. 2011. Microbially mediated plant
functional traits. Annual Review of Ecology, Evolution, and Systematics
42:23–46.
Giandomenico, A. R., G. E. Cerniglia, J. E. Biaglow, C. W. Stevens, and
C. J. Koch. 1997. The importance of sodium pyruvate in assessing damage
produced by hydrogen peroxide. Free Radical Biology & Medicine
23:426–434.
Hansen, B. L., R. de C. Pessotti, M. S. Fischer, A. Collins, L.
El-Hifnawi, M. D. Liu, and M. F. Traxler. 2020. Cooperation,
competition, and specialized metabolism in a simplified root nodule
microbiome. mBio 11:10.1128/mbio.01917-20.
Harrison, T. L., C. W. Wood, K. D. Heath, and J. R. Stinchcombe. 2017.
Geographically structured genetic variation in the Medicago
lupulina -Ensifer mutualism. Evolution 71:1787–1801.
Heberling, J. M., and D. J. Burke. 2019. Utilizing herbarium specimens
to quantify historical mycorrhizal communities. Applications in Plant
Sciences 7:e01223.
Humann, J. L., H. T. Ziemkiewicz, S. N. Yurgel, and M. L. Kahn. 2009.
Regulatory and DNA repair genes contribute to the desiccation resistance
of Sinorhizobium meliloti rm1021. Applied and Environmental
Microbiology 75:446–453.
Lai, W.-A., A. Hameed, S.-Y. Lin, M.-H. Hung, Y.-H. Hsu, Y.-C. Liu, M.
Shahina, F.-T. Shen, and C.-C. Young. 2015. Paenibacillus
medicaginis sp. nov. a chitinolytic endophyte isolated from a root
nodule of alfalfa (Medicago sativa L.). International Journal of
Systematic and Evolutionary Microbiology 65:3853–3860.
Li, W., Q. Song, R. H. Brlansky, and J. S. Hartung. 2007. Genetic
diversity of citrus bacterial canker pathogens preserved in herbarium
specimens. Proceedings of the National Academy of Sciences
104:18427–18432.
Loper, J. E., and M. N. Schroth. 1986. Influence of bacterial sources on
indole-3-acetic acid on root elongation of sugar beet. Phytopathology
76:386–389.
Martin, M. D., E. Cappellini, J. A. Samaniego, M. L. Zepeda, P. F.
Campos, A. Seguin-Orlando, N. Wales, L. Orlando, S. Y. W. Ho, F. S.
Dietrich, P. A. Mieczkowski, J. Heitman, E. Willerslev, A. Krogh, J. B.
Ristaino, and M. T. P. Gilbert. 2013. Reconstructing genome evolution in
historic samples of the Irish potato famine pathogen. Nature
Communications 4:2172.
Martínez-Hidalgo, P., P. Galindo-Villardón, J. M. Igual, and E.
Martínez-Molina. 2014. Micromonospora from nitrogen fixing nodules of
alfalfa (Medicago sativa L.). A new promising plant probiotic
bacteria. Scientific Reports 4:6389.
Martínez-Hidalgo, P., and A. M. Hirsch. 2017. The nodule microbiome:
N2-fixing rhizobia do not live alone. Phytobiomes Journal 1:70–82.
Martínez-Hidalgo, P., E. A. Humm, D. W. Still, B. Shi, M. Pellegrini, G.
de la Roca, E. Veliz, M. Maymon, P. Bru, M. Huntemann, A. Clum, K.
Palaniappan, N. Varghese, S. Mukherjee, T. B. K. Reddy, C. Daum, N. N.
Ivanova, N. C. Kyrpides, N. Shapiro, E. A. Eloe-Fadrosh, and A. M.
Hirsch. 2022. Medicago root nodule microbiomes: Insights into a
complex ecosystem with potential candidates for plant growth promotion.
Plant and Soil 471:507–526.
Molnár, A., J. Sonkoly, Á. Lovas-Kiss, R. Fekete, A. Takás, L. Somlyay,
and P. Török. 2015. Seeds of the threatened annual legume,Astragalus contortuplicatus , can survive over 130 years of dry
storage. Presalia 87:319–328.
Msaddak, A., D. Durán, M. Rejili, M. Mars, T. Ruiz-Argüeso, J. Imperial,
J. Palacios, and L. Rey. 2017. Siverse bacteria affiliated with the
genera Microvirga , Phyllobacterium , andBradyrhizobium nodulate Lupinus micranthus growing in
soils of northern Tunisia. Applied and Environmental Microbiology
83:e02820-16.
Oliver, J. D. 2005. The viable but nonculturable state in bacteria.
Journal of Microbiology (Seoul, Korea) 43 Spec No:93–100.
Park, D. S., X. Feng, S. Akiyama, M. Ardiyani, N. Avendaño, Z. Barina,
B. Bärtschi, M. Belgrano, J. Betancur, R. Bijmoer, A. Bogaerts, A. Cano,
J. Danihelka, A. Garg, D. E. Giblin, R. Gogoi, A. Guggisberg, M.
Hyvärinen, S. A. James, R. J. Sebola, T. Katagiri, J. A. Kennedy, T. S.
Komil, B. Lee, S. M. L. Lee, D. Magri, R. Marcucci, S. Masinde, D.
Melnikov, P. Mráz, W. Mulenko, P. Musili, G. Mwachala, B. E. Nelson, C.
Niezgoda, C. Novoa Sepúlveda, S. Orli, A. Paton, S. Payette, K. D.
Perkins, M. J. Ponce, H. Rainer, L. Rasingam, H. Rustiami, N. M. Shiyan,
C. S. Bjorå, J. Solomon, F. Stauffer, A. Sumadijaya, M. Thiébaut, B. M.
Thiers, H. Tsubota, A. Vaughan, R. Virtanen, T. J. S. Whitfeld, D.
Zhang, F. O. Zuloaga, and C. C. Davis. 2023. The colonial legacy of
herbaria. Nature Human Behaviour 7:1059–1068.
Petipas, R. H., M. A. Geber, and J. A. Lau. 2021. Microbe‐mediated
adaptation in plants. Ecology Letters 24:1302–1317.
Petipas, R. H., A. C. Wruck, and M. A. Geber. 2020. Microbe‐mediated
local adaptation to limestone barrens is context dependent. Ecology 101.
Radl, V., J. L. Simões-Araújo, J. Leite, S. R. Passos, L. M. V. Martins,
G. R. Xavier, N. G. Rumjanek, J. I. Baldani, and J. E. Zilli. 2014.Microvirga vignae sp. nov., a root nodule symbiotic bacterium
isolated from cowpea grown in semi-arid Brazil. International Journal of
Systematic and Evolutionary Microbiology 64:725–730.
Ristaino, J. B., C. T. Groves, and G. R. Parra. 2001. PCR amplification
of the Irish potato famine pathogen from historic specimens. Nature
411:695–697.
Rivas, R., E. Velázquez, A. Willems, N. Vizcaíno, N. S. Subba-Rao, P. F.
Mateos, M. Gillis, F. B. Dazzo, and E. Martínez-Molina. 2002. A new
species of Devosia that forms a unique nitrogen-fixing
root-nodule symbiosis with the aquatic legume Neptunia natans(l.f.) Druce. Applied and Environmental Microbiology 68:5217–5222.
Rudgers, J. A., M. E. Afkhami, L. Bell-Dereske, Y. A. Chung, K. M.
Crawford, S. N. Kivlin, M. A. Mann, and M. A. Nuñez. 2020. Climate
disruption of plant-microbe interactions. Annual Review of Ecology,
Evolution, and Systematics 51:561–586.
Stevenson, B. S., S. A. Eichorst, J. T. Wertz, T. M. Schmidt, and J. A.
Breznak. 2004. New strategies for cultivation and detection of
previously uncultured microbes. Applied and Environmental Microbiology
70:4748–4755.
Tapia-García, E. Y., V. Hernández-Trejo, J. Guevara-Luna, F. U.
Rojas-Rojas, I. Arroyo-Herrera, G. Meza-Radilla, M. S. Vásquez-Murrieta,
and P. Estrada-de Los Santos. 2020. Plant growth-promoting bacteria
isolated from wild legume nodules and nodules of Phaseolus
vulgaris L. trap plants in central and southern Mexico. Microbiological
Research 239:126522.
Trujillo, M. E., P. Alonso-Vega, R. Rodríguez, L. Carro, E. Cerda, P.
Alonso, and E. Martínez-Molina. 2010. The genus Micromonospora is
widespread in legume root nodules: the example of Lupinus
angustifolius . The ISME Journal 4:1265–1281.
Trujillo, M. E., A. Willems, A. Abril, A.-M. Planchuelo, R. Rivas, D.
Ludeña, P. F. Mateos, E. Martínez-Molina, and E. Velázquez. 2005.
Nodulation of Lupinus albus by strains of Ochrobactrum
lupini sp. nov. Applied and Environmental Microbiology 71:1318–1327.
Turkington, R., and P. B. Cavers. 1979. The Biology of Canadian Weeds
33. Medicago lupulina L. Canadian Journal of Plant Science
59:99–110.
Vincent, J. M. 1962. Influence of calcium and magnesium on the growth of
rhizobium. Journal of General Microbiology 28:653–663.
Weese, D. J., K. D. Heath, B. T. M. Dentinger, and J. A. Lau. 2015.
Long-term nitrogen addition causes the evolution of less-cooperative
mutualists: Nitrogen addition destabilizes mutualism. Evolution
69:631–642.
Weisburg, W. G., S. M. Barns, D. A. Pelletier, and D. J. Lane. 1991. 16S
ribosomal DNA amplification for phylogenetic study. Journal of
Bacteriology 173:697–703.
Wolkis, D., K. Jones, T. Flynn, M. DeMotta, and N. Rønsted. 2022.
Germination of seeds from herbarium specimens as a last conservation
resort for resurrecting extinct or critically endangered Hawaiian
plants. Conservation Science and Practice 4:e576.
Xu, L., Y. Zhang, L. Wang, W. Chen, and G. Wei. 2014. Diversity of
endophytic bacteria associated with nodules of two indigenous legumes at
different altitudes of the Qilian Mountains in China. Systematic and
Applied Microbiology 37:457–465.
Yan, J., H.-J. Chu, H.-C. Wang, J.-Q. Li, and T. Sang. 2009. Population
genetic structure of two Medicago species shaped by distinct life
form, mating system and seed dispersal. Annals of Botany 103:825–834.
Yoshida, K., V. J. Schuenemann, L. M. Cano, M. Pais, B. Mishra, R.
Sharma, C. Lanz, F. N. Martin, S. Kamoun, J. Krause, M. Thines, D.
Weigel, and H. A. Burbano. 2013. The rise and fall of thePhytophthora infestans lineage that triggered the Irish potato
famine. eLife 2:e00731.