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Article ; Online: Herbarium specimens reveal that mycorrhizal type does not mediate declining temperate tree nitrogen status over a century of environmental change.

Michaud, Talia J / Cline, Lauren C / Hobbie, Erik A / Gutknecht, Jessica L M / Kennedy, Peter G

2023 Volume 242, Issue 4, Page(s) 1717–1724

Abstract: Rising atmospheric carbon dioxide concentrations ( ... ...

Abstract	Rising atmospheric carbon dioxide concentrations (CO
MeSH term(s)	Mycorrhizae/physiology ; Nitrogen/metabolism ; Nitrogen/analysis ; Trees/microbiology ; Nitrogen Isotopes/analysis ; Carbon Dioxide/metabolism ; Plant Leaves/microbiology ; Plant Leaves/metabolism ; Minnesota ; Environment
Chemical Substances	Nitrogen (N762921K75) ; Nitrogen Isotopes ; Carbon Dioxide (142M471B3J)
Language	English
Publishing date	2023-12-10
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/nph.19452
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Article ; Online: Genetic modification of flavone biosynthesis in rice enhances biofilm formation of soil diazotrophic bacteria and biological nitrogen fixation

Yan, Dawei / Tajima, Hiromi / Cline, Lauren C. / Fong, Reedmond Y. / Ottaviani, Javier I. / Shapiro, Howard‐Yana / Blumwald, Eduardo

Plant Biotechnology Journal. 2022 Nov., v. 20, no. 11 p.2135-2148

2022

Abstract: Improving biological nitrogen fixation (BNF) in cereal crops is a long‐sought objective; however, no successful modification of cereal crops showing increased BNF has been reported. Here, we described a novel approach in which rice plants were modified ... ...

Abstract	Improving biological nitrogen fixation (BNF) in cereal crops is a long‐sought objective; however, no successful modification of cereal crops showing increased BNF has been reported. Here, we described a novel approach in which rice plants were modified to increase the production of compounds that stimulated biofilm formation in soil diazotrophic bacteria, promoted bacterial colonization of plant tissues and improved BNF with increased grain yield at limiting soil nitrogen contents. We first used a chemical screening to identify plant‐produced compounds that induced biofilm formation in nitrogen‐fixing bacteria and demonstrated that apigenin and other flavones induced BNF. We then used CRISPR‐based gene editing targeting apigenin breakdown in rice, increasing plant apigenin contents and apigenin root exudation. When grown at limiting soil nitrogen conditions, modified rice plants displayed increased grain yield. Biofilm production also modified the root microbiome structure, favouring the enrichment of diazotrophic bacteria recruitment. Our results support the manipulation of the flavone biosynthetic pathway as a feasible strategy for the induction of biological nitrogen fixation in cereals and a reduction in the use of inorganic nitrogen fertilizers.
Keywords	apigenin ; bacterial colonization ; biofilm ; biosynthesis ; biotechnology ; exudation ; genes ; genetic engineering ; grain yield ; microbiome ; nitrogen ; nitrogen fixation ; rice ; soil
Language	English
Dates of publication	2022-11
Size	p. 2135-2148.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2136367-5
ISSN	1467-7652 ; 1467-7644
ISSN (online)	1467-7652
ISSN	1467-7644
DOI	10.1111/pbi.13894
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Article: Short impact on soil microbiome of a

Adamo, Irene / Acin-Albiac, Marta / Röttjers, Sam / de Prado, Diego Rodríguez / Benito, Blas M / Zamora, Jorge / Godara, Rakesh / García-Jiménez, Beatriz / Jiang-Rempel, Panpan / Cline, Lauren C / Acedo, Alberto

Frontiers in plant science

2024 Volume 15, Page(s) 1332840

Abstract: Potato ( ...

Abstract	Potato (
Language	English
Publishing date	2024-03-12
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2024.1332840
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Article ; Online: Probing promise versus performance in longer read fungal metabarcoding.

Kennedy, Peter G / Cline, Lauren C / Song, Zewei

The New phytologist

2018 Volume 217, Issue 3, Page(s) 973–976

MeSH term(s)	Arabidopsis ; Fungi ; High-Throughput Nucleotide Sequencing ; Plant Leaves ; Sequence Analysis, DNA
Language	English
Publishing date	2018-02-22
Publishing country	England
Document type	Journal Article ; Comment
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/nph.14883
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Article ; Online: Genetic modification of flavone biosynthesis in rice enhances biofilm formation of soil diazotrophic bacteria and biological nitrogen fixation.

Yan, Dawei / Tajima, Hiromi / Cline, Lauren C / Fong, Reedmond Y / Ottaviani, Javier I / Shapiro, Howard-Yana / Blumwald, Eduardo

Plant biotechnology journal

2022 Volume 20, Issue 11, Page(s) 2135–2148

Abstract: Improving biological nitrogen fixation (BNF) in cereal crops is a long-sought objective; however, no successful modification of cereal crops showing increased BNF has been reported. Here, we described a novel approach in which rice plants were modified ... ...

Abstract	Improving biological nitrogen fixation (BNF) in cereal crops is a long-sought objective; however, no successful modification of cereal crops showing increased BNF has been reported. Here, we described a novel approach in which rice plants were modified to increase the production of compounds that stimulated biofilm formation in soil diazotrophic bacteria, promoted bacterial colonization of plant tissues and improved BNF with increased grain yield at limiting soil nitrogen contents. We first used a chemical screening to identify plant-produced compounds that induced biofilm formation in nitrogen-fixing bacteria and demonstrated that apigenin and other flavones induced BNF. We then used CRISPR-based gene editing targeting apigenin breakdown in rice, increasing plant apigenin contents and apigenin root exudation. When grown at limiting soil nitrogen conditions, modified rice plants displayed increased grain yield. Biofilm production also modified the root microbiome structure, favouring the enrichment of diazotrophic bacteria recruitment. Our results support the manipulation of the flavone biosynthetic pathway as a feasible strategy for the induction of biological nitrogen fixation in cereals and a reduction in the use of inorganic nitrogen fertilizers.
MeSH term(s)	Nitrogen Fixation/genetics ; Oryza/metabolism ; Soil ; Gene Editing ; Apigenin/metabolism ; Fertilizers ; Crops, Agricultural ; Bacteria/genetics ; Nitrogen/metabolism ; Edible Grain/metabolism ; Biofilms
Chemical Substances	Soil ; Apigenin (7V515PI7F6) ; Fertilizers ; Nitrogen (N762921K75)
Language	English
Publishing date	2022-08-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2136367-5
ISSN	1467-7652 ; 1467-7652
ISSN (online)	1467-7652
ISSN	1467-7652
DOI	10.1111/pbi.13894
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Article ; Online ; Research data: (with research data) Initial colonization, community assembly and ecosystem function: fungal colonist traits and litter biochemistry mediate decay rate.

Cline, Lauren C / Zak, Donald R

Molecular ecology

2015 Volume 24, Issue 19, Page(s) 5045–5058

Abstract: Priority effects are an important ecological force shaping biotic communities and ecosystem processes, in which the establishment of early colonists alters the colonization success of later-arriving organisms via competitive exclusion and habitat ... ...

Abstract	Priority effects are an important ecological force shaping biotic communities and ecosystem processes, in which the establishment of early colonists alters the colonization success of later-arriving organisms via competitive exclusion and habitat modification. However, we do not understand which biotic and abiotic conditions lead to strong priority effects and lasting historical contingencies. Using saprotrophic fungi in a model leaf decomposition system, we investigated whether compositional and functional consequences of initial colonization were dependent on initial colonizer traits, resource availability or a combination thereof. To test these ideas, we factorially manipulated leaf litter biochemistry and initial fungal colonist identity, quantifying subsequent community composition, using neutral genetic markers, and community functional characteristics, including enzyme potential and leaf decay rates. During the first 3 months, initial colonist respiration rate and physiological capacity to degrade plant detritus were significant determinants of fungal community composition and leaf decay, indicating that rapid growth and lignolytic potential of early colonists contributed to altered trajectories of community assembly. Further, initial colonization on oak leaves generated increasingly divergent trajectories of fungal community composition and enzyme potential, indicating stronger initial colonizer effects on energy-poor substrates. Together, these observations provide evidence that initial colonization effects, and subsequent consequences on litter decay, are dependent upon substrate biochemistry and physiological traits within a regional species pool. Because microbial decay of plant detritus is important to global C storage, our results demonstrate that understanding the mechanisms by which initial conditions alter priority effects during community assembly may be key to understanding the drivers of ecosystem-level processes.
MeSH term(s)	Biota ; DNA, Fungal/genetics ; Ecosystem ; Fungi/classification ; Fungi/physiology ; Plant Leaves/chemistry ; Plant Leaves/microbiology ; Sequence Analysis, DNA ; Soil/chemistry ; Soil Microbiology ; Trees
Chemical Substances	DNA, Fungal ; Soil
Language	English
Publishing date	2015-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083 ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.13361
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Article: Soil microbial communities are shaped by plant-driven changes in resource availability during secondary succession.

Cline, Lauren C / Zak, Donald R

Ecology

2015 Volume 96, Issue 12, Page(s) 3374–3385

Abstract: Although we understand the ecological processes eliciting changes in plant community composition during secondary succession, we do not understand whether co-occurring changes in plant detritus shape saprotrophic microbial communities in soil. In this ... ...

Abstract	Although we understand the ecological processes eliciting changes in plant community composition during secondary succession, we do not understand whether co-occurring changes in plant detritus shape saprotrophic microbial communities in soil. In this study, we investigated soil microbial composition and function across an old-field chronosequence ranging from 16 to 86 years following agricultural abandonment, as well as three forests representing potential late-successional ecosystems. Fungal and bacterial community composition was quantified from ribosomal DNA, and insight into the functional potential of the microbial community to decay plant litter was gained from shotgun metagenomics and extracellular enzyme assays. Accumulation of soil organic matter across the chronosequence exerted a positive and significant effect on fungal phylogenetic β-diversity and the activity of extracellular enzymes with lignocellulolytic activity. In addition, the increasing abundance of lignin-rich C4 grasses was positively related to the composition of fungal genes with lignocellulolytic function, thereby linking plant community composition, litter biochemistry, and microbial community function. However, edaphic properties were the primary agent shaping bacterial communities, as bacterial β-diversity and variation in functional gene composition displayed a significant and positive relationship to soil pH across the chronosequence. The late-successional forests were compositionally distinct from the oldest old fields, indicating that substantial changes occur in soil microbial communities as old fields give way to forests. Taken together, our observations demonstrate that plants govern the turnover of soil fungal communities and functional characteristics during secondary succession, due to the continual input of detritus and differences in litter biochemistry among plant species.
MeSH term(s)	Bacteria/classification ; Bacteria/genetics ; Ecosystem ; Fungi/classification ; Fungi/genetics ; Hydrogen-Ion Concentration ; Minnesota ; Phylogeny ; Plant Physiological Phenomena ; Soil/chemistry ; Soil Microbiology
Chemical Substances	Soil
Language	English
Publishing date	2015-12-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1797-8
ISSN	0012-9658
ISSN	0012-9658
DOI	10.1890/15-0184.1
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Article ; Online: Dispersal limitation structures fungal community assembly in a long-term glacial chronosequence.

Cline, Lauren C / Zak, Donald R

Environmental microbiology

2014 Volume 16, Issue 6, Page(s) 1538–1548

Abstract: Microbial communities in soil mediate biogeochemical processes; however, understanding forces shaping their composition and function remains a gap in our ecological knowledge. We investigated phylogenetic turnover and functional gene composition of ... ...

Abstract	Microbial communities in soil mediate biogeochemical processes; however, understanding forces shaping their composition and function remains a gap in our ecological knowledge. We investigated phylogenetic turnover and functional gene composition of saprotrophic fungi along a 4000-year glacial chronosequence. A direct relationship between β-diversity and geographic distance, a proxy for time since deglaciation, indicated that dispersal limitation shapes saprotrophic fungal communities. Further, we infer that dispersal limitation may also influence fungal functional properties as metabolic potential and functional richness increased with site age. Despite attempts to minimize environmental variation, a direct relationship between β-diversity and biogeochemical differences across sites indicated that environmental filtering further shapes fungal community composition. However, environmental filtering was overshadowed by the effect of dispersal limitation when tested by multiple regression. Fungal β-diversity and composition of functional genes involved in plant litter decay were unrelated, suggesting that functional traits are not phylogenetically conserved across this chronosequence. Our study suggests that dispersal limitation operates in structuring present-day fungal community composition and functional potential. Further, we demonstrate the need to integrate functional and phylogenetic approaches to more accurately portray microbial communities and their functional capacities.
MeSH term(s)	Biodiversity ; Fungi/genetics ; Genetic Variation ; Ice Cover ; Phylogeny ; Soil Microbiology
Language	English
Publishing date	2014-06
Publishing country	England
Document type	Journal Article
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.12281
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Article: Organic nitrogen addition suppresses fungal richness and alters community composition in temperate forest soils

Cline, Lauren C / Huggins, Julia A / Hobbie, Sarah E / Kennedy, Peter G

Soil biology & biochemistry. 2018 Oct., v. 125

2018

Abstract: Human-driven increases in bioavailable nitrogen over the last century have revealed the critical need to understand how nitrogen availability influences terrestrial ecosystems. In contrast to widespread evidence that increasing inorganic nitrogen ... ...

Abstract	Human-driven increases in bioavailable nitrogen over the last century have revealed the critical need to understand how nitrogen availability influences terrestrial ecosystems. In contrast to widespread evidence that increasing inorganic nitrogen strongly influences the diversity and composition of plant and microbial communities, the effect of organic nitrogen addition, the predominant form of nitrogen in soils, remains less clear. In this study, we conducted a field experiment manipulating both the amount and composition of soil organic nitrogen present in soil fungal in-growth bags, followed by molecular characterization of fungal communities after a four-month incubation. Saprotrophic and ectomycorrhizal fungi readily colonized experimental in-growth bags, indicating a broad overlap in the fundamental niches of these two functional guilds. Increases in labile forms of organic nitrogen resulted in sharp declines in species richness and diversity across fungal guilds, as well as notable shifts in fungal community composition. The relative abundance of fungi classified as molds and yeasts peaked where organic nitrogen was both high and most labile, whereas slower-growing saprotrophic and ectomycorrhizal fungi were more abundant in the non-amended treatments. Taken together, our results indicate that similar to inorganic nitrogen, increasing the amount of organic nitrogen can dramatically alter the richness and composition of fungal communities in temperate forest soils.
Keywords	bags ; community structure ; field experimentation ; forest soils ; fungal communities ; molds (fungi) ; mycorrhizal fungi ; niches ; nitrogen ; saprotrophs ; soil organic nitrogen ; temperate forests ; terrestrial ecosystems ; yeasts
Language	English
Dates of publication	2018-10
Size	p. 222-230.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	280810-9
ISSN	0038-0717
ISSN	0038-0717
DOI	10.1016/j.soilbio.2018.07.008
Database	NAL-Catalogue (AGRICOLA)

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Article ; Research data: (with research data) Ecological and functional effects of fungal endophytes on wood decomposition

Cline, Lauren C / Jonathan S. Schilling / Jon Menke / Emily Groenhof / Peter G. Kennedy

Functional ecology. 2018 Jan., v. 32, no. 1

2018

Abstract: Despite the central role of saprotrophic fungi in wood decomposition and terrestrial carbon cycling, the diversity and functioning of wood endophytes (i.e. fungi that asymptomatically colonize living plant tissue) on decay remains poorly understood. In a ...

Abstract	Despite the central role of saprotrophic fungi in wood decomposition and terrestrial carbon cycling, the diversity and functioning of wood endophytes (i.e. fungi that asymptomatically colonize living plant tissue) on decay remains poorly understood. In a 4âyear field experiment in a boreal forest in the upper midwestern United States, we investigated whether endophytes influenced fungal community structure and subsequent wood decomposition via priority effects. We compared decay of sterilized and nonâsterilized birch (BetulaÂ papyrifera) logs using both highâthroughput sequencing and wood physiochemical analyses (i.e. density loss, dilute alkali solubility, ratio of lignin loss relative to density loss). Endophyte presence significantly altered initial fungal species composition during the first 2Â years and enhanced mass loss over the experiment's duration. Results suggest that following tree death the immediate utilization of organic substrates by wood endophytes significantly alters establishment patterns of later arriving fungal saprotrophs. Independent of endophyte presence, white rot was the wood decay outcome at all sampling times, despite an initial presence of both brown and white rot fungi. Collectively, these findings demonstrate that wood endophytes can affect early community assembly and subsequent decay rates, although environmental filtering leads to consistent selection for fungi with ligninâtargeted decay strategies. A plain language summary is available for this article.
Keywords	Betula papyrifera ; boreal forests ; carbon cycle ; community structure ; decayed wood ; endophytes ; field experimentation ; fungal communities ; high-throughput nucleotide sequencing ; lignin ; plant tissues ; saprotrophs ; solubility ; species diversity ; tree mortality ; white-rot fungi ; Midwestern United States
Language	English
Dates of publication	2018-01
Size	p. 181-191.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Research data
Note	JOURNAL ARTICLE
ZDB-ID	2020307-X
ISSN	1365-2435 ; 0269-8463 ; 0269-8463
ISSN (online)	1365-2435
ISSN	0269-8463
DOI	10.1111/1365-2435.12949
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