patrickbdevaney/mia9 · Datasets at Hugging Face

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65. Rosling, A.; Cox, F.; Cruz-Martinez, K.; Ihrmark, K.; Grelet, G.-A.; Lindahl, B.D.; Menkis, A.; James, T.Y.
Archaeorhizomycetes: Unearthing an ancient class of ubiquitous soil fungi. Science 2011, 333, 876–879.
[CrossRef]
66. Morgenstern, I.; Klopman, S.; Hibbett, D.S. Molecular evolution and diversity of lignin degrading heme
peroxidases in the Agaricomycetes. J. Mol. Evol. 2008, 66, 243–257. [CrossRef]
67. Schadt, C.W.; Martin, A.P.; Lipson, D.A.; Schmidt, S.K. Seasonal dynamics of previously unknown fungal
lineages in tundra soils. Science 2003, 301, 1359–1361. [CrossRef]
68. Morón-Ríos, A.; Gómez-Cornelio, S.; Ortega-Morales, B.O.; De la Rosa-García, S.; Partida-Martínez, L.P.;
Quintana, P.; Alayón-Gamboa, J.A.; Cappello-García, S.; González-Gómez, S. Interactions between abundant
fungal species influence the fungal community assemblage on limestone. PLoS ONE 2017, 12, e0188443.
[CrossRef]
69. Subedi, S.C.; Ross, M.S.; Scinto, L.J. Nutrient Limitation in Two Everglades Tree Species Planted on
Constructed Tree Islands. Wetlands 2012, 32, 1163–1173. [CrossRef]
70. Sullivan, P.L.; Price, R.M.; Ross, M.S.; Scinto, L.J.; Stoffella, S.L.; Cline, E.; Dreschel, T.W.; Sklar, F.H. Hydrologic
processes on tree islands in the Everglades (Florida, USA): Tracking the effects of tree establishment and
growth. Hydrogeol. J. 2011, 19, 367–378. [CrossRef]
71. Estrada-Medina, H.; Canto-Canché, B.B.; De Los Santos-Briones, C.; O’Connor-Sánchez, A. Yucatán in black
and red: Linking edaphic analysis and pyrosequencing-based assessment of bacterial and fungal community
structures in the two main kinds of soil of Yucatán State. Microbiol. Res. 2016, 188, 23–33. [CrossRef]
[PubMed]
72. Rose, S.L. Mycorrhizal associations of some actinomycete nodulated nitrogen-fixing plants. Can. J. Bot.
1980, 58, 1449–1454. [CrossRef]
73. Ma, S.; Verheyen, K.; Props, R.; Wasof, S.; Vanhellemont, M.; Boeckx, P.; Boon, N.; De Frenne, P.
Plant and soil microbe responses to light, warming and nitrogen addition in a temperate forest. Funct. Ecol.
2018, 32, 1293–1303. [CrossRef]
74. Bartemucci, P.; Messier, C.; Canham, C.D. Overstory influences on light attenuation patterns and
understory plant community diversity and composition in southern boreal forests of Quebec. Can. J. For. Res.
2006, 36, 2065–2079. [CrossRef]
75. Kulmatiski, A.; Beard, K.H. Long-term plant growth legacies overwhelm short-term plant growth effects on
soil microbial community structure. Soil Biol. Biochem. 2011, 43, 823–830. [CrossRef]
76. McGuire, K.L.; Fierer, N.; Bateman, C.; Treseder, K.K.; Turner, B.L. Fungal community composition in
neotropical rain forests: The influence of tree diversity and precipitation. Microb. Ecol. 2012, 63, 804–812.
[CrossRef]
77. Broeckling, C.D.; Broz, A.K.; Bergelson, J.; Manter, D.K.; Vivanco, J.M. Root exudates regulate soil fungal
community composition and diversity. Appl. Environ. Microbiol. 2008, 74, 738–744. [CrossRef]
78. Kong, C.H.; Wang, P.; Zhao, H.; Xu, X.H.; Zhu, Y.D. Impact of allelochemical exuded from allelopathic rice
on soil microbial community. Soil Biol. Biochem. 2008, 40, 1862–1869. [CrossRef]
79. Chapman, S.K.; Newman, G.S. Biodiversity at the plant–soil interface: Microbial abundance and community
structure respond to litter mixing. Oecologia 2010, 162, 763–769. [CrossRef]
Diversity 2020, 12, 0324 17 of 17
80. Wang, J.; Chen, C.; Ye, Z.; Li, J.; Feng, Y.; Lu, Q. Relationships Between Fungal and Plant Communities
Differ Between Desert and Grassland in a Typical Dryland Region of Northwest China. Front. Microbiol.
2018, 9, 2327. [CrossRef]
81. Voˇríšková, J.; Baldrian, P. Fungal community on decomposing leaf litter undergoes rapid successional
changes. ISME J. 2013, 7, 477–486. [CrossRef] [PubMed]
82. Sheldrake, M.; Rosenstock, N.P.; Revillini, D.; Olsson, P.A.; Mangan, S.; Sayer, E.J.; Wallander, H.; Turner, B.L.;
Tanner, E.V.J. Arbuscular mycorrhizal fungal community composition is altered by long-term litter removal
but not litter addition in a lowland tropical forest. New Phytol. 2017, 214, 455–467. [CrossRef] [PubMed]
83. Bittebiere, A.; Vandenkoornhuyse, P.; Maluenda, E.; Gareil, A.; Dheilly, A.; Coudouel, S.; Bahin, M.; Mony, C.
Past spatial structure of plant communities determines arbuscular mycorrhizal fungal community assembly.
J. Ecol. 2020, 108, 546–560. [CrossRef]
84. Rashid, M.I.; Mujawar, L.H.; Shahzad, T.; Almeelbi, T.; Ismail, I.M.I.; Oves, M. Bacteria and fungi can contribute
to nutrients bioavailability and aggregate formation in degraded soils. Microbiol. Res. 2016, 183, 26–41.
[CrossRef]
85. Matulich, K.L.; Martiny, J.B.H. Microbial composition alters the response of litter decomposition to
environmental change. Ecology 2015, 96, 154–163. [CrossRef]
86. Maron, J.L.; Marler, M.; Klironomos, J.N.; Cleveland, C.C. Soil fungal pathogens and the relationship between
plant diversity and productivity. Ecol. Lett. 2011, 14, 36–41. [CrossRef]
87. Van der Heijden, M.G.A.; Boller, T.; Wiemken, A.; Sanders, I.R. Different arbsucular mycorrhizal fungal
species are potential determinants of plant community structure. Ecology 1998, 79, 2082–2091. [CrossRef]
88. Bartelt-Ryser, J.; Joshi, J.; Schmid, B.; Brandl, H.; Balser, T. Soil feedbacks of plant diversity on soil microbial
communities and subsequent plant growth. Perspect. Plant Ecol. Evol. Syst. 2005, 7, 27–49. [CrossRef]
89. Arnold, A.E.; Elizabeth Arnold, A. Understanding the diversity of foliar endophytic fungi: Progress,
challenges, and frontiers. Fungal Biol. Rev. 2007, 21, 51–66. [CrossRef]
90. Crowther, T.W.; Boddy, L.; Hefin Jones, T. Functional and ecological consequences of saprotrophic
fungus–grazer interactions. ISME J. 2012, 6, 1992–2001. [CrossRef]
91. Dreschel, T.W.; Cline, E.A.; Hill, S.D. Everglades tree island restoration: Testing a simple tree planting
technique patterned after a natural process. Restor. Ecol. 2017, 25, 696–704. [CrossRef]
92. Amend, A.S.; Seifert, K.A.; Bruns, T.D. Quantifying microbial communities with 454 pyrosequencing:
Does read abundance count? Mol. Ecol. 2010, 19, 5555–5565. [CrossRef] [PubMed]
93. Troskie, A.M.; Vlok, N.M.; Rautenbach, M. A novel 96-well gel-based assay for determining antifungal
activity against filamentous fungi. J. Microbiol. Methods 2012, 91, 551–558. [CrossRef] [PubMed]
94. Lee, Y.-J.; van Nostrand, J.D.; Tu, Q.; Lu, Z.; Cheng, L.; Yuan, T.; Deng, Y.; Carter, M.Q.; He, Z.; Wu, L.; et al.
The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities.
ISME J. 2013, 7, 1974–1984. [CrossRef]
95. Carvalhais, L.C.; Dennis, P.G.; Tyson, G.W.; Schenk, P.M. Application of metatranscriptomics to soil
environments. J. Microbiol. Methods 2012, 91, 246–251. [CrossRef]
© 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access
article distributed under the terms and conditions of the Creative Commons Attribution
(CC BY) license (http://creativecommons.org/licenses/by/4.0/).

ORIGINAL RESEARCH
published: 23 July 2021
doi: 10.3389/fmars.2021.633240
Edited by:
Frank S. Gilliam,
University of West Florida,
United States
Reviewed by:
Jane Caffrey,
University of West Florida,
United States
Wade H. Jeffrey,
University of West Florida,
United States
*Correspondence:
Jonathan R. Rodemann
Jrode010@fiu.edu
Specialty section:
This article was submitted to

65. Rosling, A.; Cox, F.; Cruz-Martinez, K.; Ihrmark, K.; Grelet, G.-A.; Lindahl, B.D.; Menkis, A.; James, T.Y.

Archaeorhizomycetes: Unearthing an ancient class of ubiquitous soil fungi. Science 2011, 333, 876–879.

[CrossRef]

66. Morgenstern, I.; Klopman, S.; Hibbett, D.S. Molecular evolution and diversity of lignin degrading heme

peroxidases in the Agaricomycetes. J. Mol. Evol. 2008, 66, 243–257. [CrossRef]

67. Schadt, C.W.; Martin, A.P.; Lipson, D.A.; Schmidt, S.K. Seasonal dynamics of previously unknown fungal

lineages in tundra soils. Science 2003, 301, 1359–1361. [CrossRef]

68. Morón-Ríos, A.; Gómez-Cornelio, S.; Ortega-Morales, B.O.; De la Rosa-García, S.; Partida-Martínez, L.P.;

Quintana, P.; Alayón-Gamboa, J.A.; Cappello-García, S.; González-Gómez, S. Interactions between abundant

fungal species influence the fungal community assemblage on limestone. PLoS ONE 2017, 12, e0188443.

[CrossRef]

69. Subedi, S.C.; Ross, M.S.; Scinto, L.J. Nutrient Limitation in Two Everglades Tree Species Planted on

Constructed Tree Islands. Wetlands 2012, 32, 1163–1173. [CrossRef]

70. Sullivan, P.L.; Price, R.M.; Ross, M.S.; Scinto, L.J.; Stoffella, S.L.; Cline, E.; Dreschel, T.W.; Sklar, F.H. Hydrologic

processes on tree islands in the Everglades (Florida, USA): Tracking the effects of tree establishment and

growth. Hydrogeol. J. 2011, 19, 367–378. [CrossRef]

71. Estrada-Medina, H.; Canto-Canché, B.B.; De Los Santos-Briones, C.; O’Connor-Sánchez, A. Yucatán in black

and red: Linking edaphic analysis and pyrosequencing-based assessment of bacterial and fungal community

structures in the two main kinds of soil of Yucatán State. Microbiol. Res. 2016, 188, 23–33. [CrossRef]

[PubMed]

72. Rose, S.L. Mycorrhizal associations of some actinomycete nodulated nitrogen-fixing plants. Can. J. Bot.

1980, 58, 1449–1454. [CrossRef]

73. Ma, S.; Verheyen, K.; Props, R.; Wasof, S.; Vanhellemont, M.; Boeckx, P.; Boon, N.; De Frenne, P.

Plant and soil microbe responses to light, warming and nitrogen addition in a temperate forest. Funct. Ecol.

2018, 32, 1293–1303. [CrossRef]

74. Bartemucci, P.; Messier, C.; Canham, C.D. Overstory influences on light attenuation patterns and

understory plant community diversity and composition in southern boreal forests of Quebec. Can. J. For. Res.

2006, 36, 2065–2079. [CrossRef]

75. Kulmatiski, A.; Beard, K.H. Long-term plant growth legacies overwhelm short-term plant growth effects on

soil microbial community structure. Soil Biol. Biochem. 2011, 43, 823–830. [CrossRef]

76. McGuire, K.L.; Fierer, N.; Bateman, C.; Treseder, K.K.; Turner, B.L. Fungal community composition in

neotropical rain forests: The influence of tree diversity and precipitation. Microb. Ecol. 2012, 63, 804–812.

[CrossRef]

77. Broeckling, C.D.; Broz, A.K.; Bergelson, J.; Manter, D.K.; Vivanco, J.M. Root exudates regulate soil fungal

community composition and diversity. Appl. Environ. Microbiol. 2008, 74, 738–744. [CrossRef]

78. Kong, C.H.; Wang, P.; Zhao, H.; Xu, X.H.; Zhu, Y.D. Impact of allelochemical exuded from allelopathic rice

on soil microbial community. Soil Biol. Biochem. 2008, 40, 1862–1869. [CrossRef]

79. Chapman, S.K.; Newman, G.S. Biodiversity at the plant–soil interface: Microbial abundance and community

structure respond to litter mixing. Oecologia 2010, 162, 763–769. [CrossRef]

Diversity 2020, 12, 0324 17 of 17

80. Wang, J.; Chen, C.; Ye, Z.; Li, J.; Feng, Y.; Lu, Q. Relationships Between Fungal and Plant Communities

Differ Between Desert and Grassland in a Typical Dryland Region of Northwest China. Front. Microbiol.

2018, 9, 2327. [CrossRef]

81. Voˇríšková, J.; Baldrian, P. Fungal community on decomposing leaf litter undergoes rapid successional

changes. ISME J. 2013, 7, 477–486. [CrossRef] [PubMed]

82. Sheldrake, M.; Rosenstock, N.P.; Revillini, D.; Olsson, P.A.; Mangan, S.; Sayer, E.J.; Wallander, H.; Turner, B.L.;

Tanner, E.V.J. Arbuscular mycorrhizal fungal community composition is altered by long-term litter removal

but not litter addition in a lowland tropical forest. New Phytol. 2017, 214, 455–467. [CrossRef] [PubMed]

83. Bittebiere, A.; Vandenkoornhuyse, P.; Maluenda, E.; Gareil, A.; Dheilly, A.; Coudouel, S.; Bahin, M.; Mony, C.

Past spatial structure of plant communities determines arbuscular mycorrhizal fungal community assembly.

J. Ecol. 2020, 108, 546–560. [CrossRef]

84. Rashid, M.I.; Mujawar, L.H.; Shahzad, T.; Almeelbi, T.; Ismail, I.M.I.; Oves, M. Bacteria and fungi can contribute

to nutrients bioavailability and aggregate formation in degraded soils. Microbiol. Res. 2016, 183, 26–41.

[CrossRef]

85. Matulich, K.L.; Martiny, J.B.H. Microbial composition alters the response of litter decomposition to

environmental change. Ecology 2015, 96, 154–163. [CrossRef]

86. Maron, J.L.; Marler, M.; Klironomos, J.N.; Cleveland, C.C. Soil fungal pathogens and the relationship between

plant diversity and productivity. Ecol. Lett. 2011, 14, 36–41. [CrossRef]

87. Van der Heijden, M.G.A.; Boller, T.; Wiemken, A.; Sanders, I.R. Different arbsucular mycorrhizal fungal

species are potential determinants of plant community structure. Ecology 1998, 79, 2082–2091. [CrossRef]

88. Bartelt-Ryser, J.; Joshi, J.; Schmid, B.; Brandl, H.; Balser, T. Soil feedbacks of plant diversity on soil microbial

communities and subsequent plant growth. Perspect. Plant Ecol. Evol. Syst. 2005, 7, 27–49. [CrossRef]

89. Arnold, A.E.; Elizabeth Arnold, A. Understanding the diversity of foliar endophytic fungi: Progress,

challenges, and frontiers. Fungal Biol. Rev. 2007, 21, 51–66. [CrossRef]

90. Crowther, T.W.; Boddy, L.; Hefin Jones, T. Functional and ecological consequences of saprotrophic

fungus–grazer interactions. ISME J. 2012, 6, 1992–2001. [CrossRef]

91. Dreschel, T.W.; Cline, E.A.; Hill, S.D. Everglades tree island restoration: Testing a simple tree planting

technique patterned after a natural process. Restor. Ecol. 2017, 25, 696–704. [CrossRef]

92. Amend, A.S.; Seifert, K.A.; Bruns, T.D. Quantifying microbial communities with 454 pyrosequencing:

Does read abundance count? Mol. Ecol. 2010, 19, 5555–5565. [CrossRef] [PubMed]

93. Troskie, A.M.; Vlok, N.M.; Rautenbach, M. A novel 96-well gel-based assay for determining antifungal

activity against filamentous fungi. J. Microbiol. Methods 2012, 91, 551–558. [CrossRef] [PubMed]

94. Lee, Y.-J.; van Nostrand, J.D.; Tu, Q.; Lu, Z.; Cheng, L.; Yuan, T.; Deng, Y.; Carter, M.Q.; He, Z.; Wu, L.; et al.

The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities.

ISME J. 2013, 7, 1974–1984. [CrossRef]

95. Carvalhais, L.C.; Dennis, P.G.; Tyson, G.W.; Schenk, P.M. Application of metatranscriptomics to soil

environments. J. Microbiol. Methods 2012, 91, 246–251. [CrossRef]

article distributed under the terms and conditions of the Creative Commons Attribution

(CC BY) license (http://creativecommons.org/licenses/by/4.0/).

ORIGINAL RESEARCH

published: 23 July 2021

doi: 10.3389/fmars.2021.633240

Edited by:

Frank S. Gilliam,

University of West Florida,

United States

Reviewed by:

Jane Caffrey,

University of West Florida,

United States

Wade H. Jeffrey,

University of West Florida,

United States

*Correspondence:

Jonathan R. Rodemann

Jrode010@fiu.edu

Specialty section:

This article was submitted to