2023
Le, N., J. Heras, M.J. Herrera, D.P. German, and L.T. Crummett (2023)
The genome of Anoplarchus purpurescens (Stichaeidae) reflects its
carnivorous diet.
Molecular Genetics and Genomics:
In press [pdf]
Rankins, D.R., M.J. Herrera, M.P. Christensen, A. Chen, N.Z. Hood, J.
Heras, and D.P. German (2023) When Digestive physiology doesn't match
"diet":
Lumpenus sagitta is an "omnivore" with a carnivorous gut.
Comparative Biochemistry and Physiology A 285: 111508
[pdf]
German, D.P., and M.S. Hedrick (2023) Editorial on "Adaptations of the nutrient supply organs that fuel the fire of life".
Comparative Biochemistry and Physiology A 278: 111371
[pdf]
Wehrle, B.A., D.P. German (2023) Reptilian digestive efficiency: past, present, and future.
Comparative Biochemistry and Physiology A 277:
111369
[pdf]
Pham, T., H. Hong, B. Swig, D.P. German, K.M. Connor. (2023) Elevated
aerial temperature modulates digestive enzyme activities in
Mytilus californianus.
Comparative Biochemistry and Physiology B 265: 110865
[pdf]
Wright, D.B., M. Escalona, M.P.A. Marimuthu, R. Sahasrabudhe, O.
Nguyen, S. Sacco, E. Beraut, E. Toffelmier, C. Miller, H.B. Shaffer, G.
Bernardi, and D.P. German. (2023) Reference genome of the Monkeyface
Prickleback,
Cebidichthys violaceus (Stichaeidae, Perciformes), a model California intertidal fish.
Journal of Heredity [pdf]
2022
Leigh, S.C., C. Catabay, D.P. German (2022) Sustained changes in
digestive physiology and microbiome across sequential
generations of zebrafish fed different diets.
Comparative Biochemistry and Physiology A 273: 111285
[pdf]
Lemieux-Labonte, V. C. Vigliotti, S. Dowd, Z. Tadic, B. Wehrle, P.
Lopez, E. Baptese, F.J. Lapointe, D.P. German, A. Herrel. (2022)
Proximate Drivers of population level lizard gut microbial diversity:
impacts of diet, insularity, and local environment.
Microorganisms 10: 1550
[pdf]
Frederick, A.R., A.M. Lee, B.A. Wehrle, C.C. Catabay, D.R. Rankins,
K.D. Clements, D.P. German (2022) Abalone under moderate heat stress
have elevated metabolic rates and changes to digestive enzyme activities
.
Comparative Biochemistry and Physiology A: 111230
[pdf]
Williams, S. M. Stoslopf, R. Francis-Floyd, L. Koutsos, E. Direnfeld,
T. Harmon, E. Cicotello, D.P. German, K. Semmen, J. Keaffaber, F.
Olea-Popelka, S. Livingston, K. Sullivan, L. Cersosimo, E. Valdez
(2022) Recommendations and action plans to improve ex-situ nutrition
and health of marine teleosts.
Journal of Aquatic Animal Health 34: 68-81
[pdf]
H
errera, M.J., J. Heras, D.P. German (2022) Comparative transcriptomics
reveal tissue level specialization towards diet in prickleback fishes
. Journal of Comparative Physiology B 192: 275-295 [pdf]
Frederick, A.R., J. Heras, C.S. Friedman, D.P. German (2022) Withering
syndrome induced gene expression changes and a de-novo transcriptome
for pinto abalone,
Haliotis kamtschatkana.
Comparative Biochemistry and Physiology D: 100930
[pdf]
2021
German, D.P., M.R. Rose. (2021) Notes towards an evolutionary biology of nutrition. In:
Nutrition, Food, and Diet in Ageing and Longevity, S.I.S Rattan, and G. Kaur (Eds.). Springer Nature, Switzerland. Please inquire about a copy of this chapter.
Leigh, S.C., A.P. Summers, S.L. Hoffmann, and D.P. German (2021) Shark spiral intestines may operate as Tesla Valves.
Proceedings of the Royal Society B 288 20211359
[pdf]
Leigh, S.C., Y.P. Papastamatiou, and D.P. German (2021) Gut microbial diversity and digestive function of an omnivorous shark.
Marine Biology 168: 55
[pdf]
Nguyen-Phuc, B.Q., C. Demetropolous,
S. Stewart, P. Saffarinia, J.D. Bastian-Salgado, E. Hawkins, A.R.
Frederick, and D.P. German. (2021) Nutritional physiology of Santa Ana
Sucker, Catostomus santaanae: a threatened freshwater fish endemic to
southern California. Acta Zoologica 102: 105-116 [pdf]
2020
Wehrle, B.A., A. Herrel, B-Q Nguyen-Phuc, S. Maldanado Jr., R.K. Dang,
R. Agnihotri, Z. Tadić, and D.P. German. (2020) Rapid dietary shift in
Podarcis siculus resulted in localized changes in gut function.
Physiological and Biochemical Zoology 93: 396-415
[pdf]
McCauley, M., D.P. German, N.K. Lujan, and C.R. Jackson. (2020) Gut
microbiomes of sympatric Amazonian wood-eating catfishes (Loricariidae)
reflect host identity and little role in wood digestion.
Ecology and Evolution 10: 7117-7128.
[pdf]
Heras, J., M. Chakraborty, J.J.
Emerson, and D.P. German. (2020) Genomic and biochemical evidence of
dietary adaptation in a marine herbivorous fish. Proceedings of the Royal Society B 287: 20192327. [pdf] Supplemental Material
2018
Leigh, S.C., Y.P. Papastamatiou,
and D.P. German (2018) Seagrass digestion by a notorious
"carnivore". Proceedings of the
Royal Society B 285: 20181583 [pdf]
Supplemental
Material Supplemental
Methods
Santos, A.*, A.R. Frederick*,
B.A.
Higgins, A. Carrillo, A. Carter, K.M. Dickson, D.P. German, and M.H.
Horn (2018) Egg cannibalism in fishes: the beach-spawning grunion (Leuresthes tenuis) eats and digests
its own eggs. Journal of Fish Biology
93: 282-289 [pdf]
*these authors contributed equally to this article.
Leigh, S.C., B-Q. Nguyen-Phuc,
and D.P. German (2018) The effects of protein and fiber content
on gut structure and function in zebrafish (Danio rerio). Journal of Comparative Physiology B
188: 237-253 [pdf] Supplemental
Table 1
2017
Leigh, S.C., Y.P. Papastamatiou,
and D.P. German (2017) The nutritional physiology of sharks. Reviews in Fish Biology and Fisheries
27: 561-585 [pdf]
German, D.P., D. Raven, and N.M.
Aguilar-Roca (2017) Floating fishes: an activity investigating
overfishing, buoyancy, and gas compressibility. American Biology Teacher 79: 49-54 [pdf]
Supplemental
Materials
Clements, K.D., D.P. German, J.
Piche, A. Tribollet, and J.H. Choat. (2017) Integrating ecological
roles and trophic diversification on coral reefs: multiple lines of
evidence identify parrotfishes as microphages.
Biological Journal of the
Linnean Society 120: 729-751 [pdf]
2016
Connor, K., A. Sung, N.S.
Garcia, A. Gracey, and D.P. German (2016) Modulation of digestive
physiology and biochemistry in
Mytilus
californianus in response to
feeding level acclimation and intertidal microhabitat.
Biology Open 5:
1200-1210
[pdf]
German, D.P.*, D.M. Foti*, J.
Heras, H. Amerkhanian, and B.L. Lockwood (2016) Elevated gene copy
number does not always explain elevated amylase activities in fishes.
Physiological and Biochemical
Zoology 89: 277-293 *These authors contributed equally to this
work [pdf]
Supplemental
materials
2015
Jhaveri, P., Y. Papastamatiou,
and D.P. German (2015) Digestive enzyme activities in the guts of
bonnethead sharks (Sphyrna tiburo)
provide insight into their digestive strategy and evidence
for microbial digestion in their hindguts. Comparative Biochemistry and Physiology A:
189: 76-83 [pdf]
German, D.P., and S.D. Allison
(2015)
Drying and substrate concentrations interact to inhibit decomposition
of carbon substrates added to combusted Inceptisols from a boreal
forest. Biology and Fertility of
Soils 51: 525-533 [pdf]
Sullam, K.E., C.M. Dalton, J.A.
Russell, S.S. Kilham, R. El-Sabaawi, D.P. German, and A.S. Flecker.
(2015) Changes in digestive traits and body nutritional composition
accommodate a trophic niche shift in Trinidadian guppies. Oecologia 177: 245-257 [pdf]
German, D.P., A. Sung, P.K. Jhaveri, and R. Agnihotri (2015). More than
one way to be an herbivore: convergent evolution of herbivory using
different digestive strategies in prickleback fishes (family
Stichaeidae).
Zoology 118:
161-170
[pdf]
Supplemental
materials Elsevier
write up about the paper
2014
Allison,
S.D., S.S. Chacon, and
D.P. German (2014) Substrate concentration constraints on microbial
decomposition. Soil Biology and
Biochemistry 79: 43-49. [pdf]
German, D.P., A.K. Gawlicka, and
M.H. Horn (2014) Evolution of ontogenetic dietary shifts and associated
gut features in prickleback fishes (Teleostei: Stichaeidae). Comparative Biochemistry and Physiology B 168:
12-18 [pdf]
Kim, K.H., M.H. Horn, A.E. Sosa,
and D.P. German (2014) Sequence of an a-amylase gene in four related
species of prickleback fishes (Teleostei: Stichaeidae): ontogenetic,
dietary, and species-level effects. Journal
of Comparative Physiology B 184: 221-234 [pdf]
2013
Bach, C.E., D.D. Warnock, D.J.
Van Horn, M.N. Weintraub, R.L. Sinsabaugh, S.D. Allison, and D.P.
German (2013) Measuring phenol oxidase and peroxidase activities
with pyrogallol, l-DOPA, and ABTS: effect of assay conditions and soil
type. Soil Biology & Biochemistry
67: 183-191 [pdf]
Supplementary Tables
Alster, C.J., D.P. German, Y.
Lu, and
S.D. Allison (2013)
Microbial enzymatic response to drought and to nitrogen addition
in a southern California grassland. Soil
Biology & Biochemistry 64: 68-79 [pdf]
2012
German,
D.P., M.N.
Weintraub, A.S. Grandy, C.L. Lauber, Z.L.
Rinkes and
S.D. Allison (2012)
Response to Steen and Ziergovel's comment on "Optimization of
hydrolytic and oxidative enzyme methods for
ecosystem studies". Soil
Biology & Biochemistry 48: 198-199 [pdf]
German, D.P., K.R.B. Marcelo,
M.M. Stone and S.D. Allison (2012) The Michaelis-Menten kinetics of
soil extracellular enzymes in response to temperature: a
cross-latitudinal study. Global
Change Biology 18: 1468-1479 [pdf]
Stone, M.M., M.S. Weiss, C.L.
Goodale, M.B. Adams, I.J. Fernandez, D.P. German, and S.D. Allison
(2012) Temperature sensitivity of soil enzyme kinetics under
N-fertilization in two temperate forests. Global Change Biology 18: 1173-1184
[pdf]
2011
Lujan, N.K., D.P. German, and
K.L. Winemiller (2011) Do wood grazing fishes partition their
niche? Morphological and isotopic evidence for trophic segregation in
Neotropical Loricariidae. Functional
Ecology 25: 1327-1338 [pdf]
German,
D.P., M.N.
Weintraub, A.S. Grandy, C.L. Lauber, Z.L.
Rinkes and
S.D. Allison (2011)
Optimization of hydrolytic and oxidative enzyme methods for
ecosystem studies.
Soil
Biology & Biochemistry 43: 1387-1397 [pdf]
Please see the Corrigendum to this
article, in which we correct two of the equations: equation 3
and equation 5 [pdf]
A Web of Science "highly cited
paper"
German,
D.P., S. Chacon and S.D. Allison (2011) Substrate
concentration and enzyme allocation can affect rates of microbial
decomposition.
Ecology 92: 1471-1480 [pdf]
Day,
R.D., D.P. German, J.M.
Manjakasy, I. Farr, J. Hansen and I.R. Tibbetts (2011) Enzymatic
digestion in stomachless fishes: how a simple gut accommodates both
carnivory and herbivory. Journal of
Comparative Physiology B 181: 603-613 [pdf]
(New Scientist did a story on
this article. You can see it here.)
German,
D.P. (2011) Digestive efficiency. In: Encyclopedia
of Fish Physiology, From Genome to Environment,
Farrell
A.P., J.J. Cech, J.G. Richards, and E.D. Stevens (Eds). Elsevier, San
Diego,
CA (due to copyright law, I can't provide a pdf of this chapter
for free on my website, but you can ask me for it! Send me an
e-mail to request a pdf)
Day,
R.D., D.P.
German and I.R.
Tibbetts (2011)
Why can't young fish eat plants?
Neither digestive
enzymes nor gut development preclude herbivory in the young of a
stomachless
marine herbivorous fish. Comparative
Biochemistry and Physiology B 158:
23-29 [pdf]
2010
German,
D.P. and R.D. Miles (2010) Stable carbon and
nitrogen incorporation
in blood and fin tissue of the catfish Pterygoplichthys
disjunctivus
(Siluriformes, Loricariidae). Environmental
Biology of Fishes 89: 117-133
[pdf]
Supplemental Figure
S1
Supplemental Figure
S2
German,
D.P., D.T. Neuberger, M.N. Callahan, N.R. Lizardo and D.H. Evans
(2010) Feast to famine: the effects of food quality and quantity on the
gut
structure and function of a detritivorous catfish (Teleostei:
Loricariidae). Comparative
Biochemistry and Physiology A 155:
281-293 [pdf]
German, D.P., B.C. Nagle, J.M.
Villeda, A.M. Ruiz, A.W. Thomson, S.
Contreras-Balderas and D.H. Evans (2010) Evolution of
herbivory
in a carnivorous clade of minnows (Teleostei: Cyprinidae): effects on
gut size and digestive physiology. Physiological and
Biochemical
Zoology 83: 1-18 [pdf]
Supplemental Table
A1
Supplemental Figure
A1
Note: the value for Campostoma
anomalum Zihler's Index (ZI)
in Table
3
of this paper should be 20.76,
not 2.76, as is listed. This mistake that was missed in the
proofing process. Please make a note of this error on your
copy
of this article.
2009
German,
D.P. (2009) Inside the guts of wood-eating catfishes: can they digest
wood? Journal of
Comparative Physiology B 179:
1011-1023 [pdf]
German,
D.P. and R.A. Bittong (2009) Digestive enzyme activities and
gastrointestinal fermentation in wood-eating
catfishes. Journal
of Comparative Physiology B 179:
1025-1042
[pdf]
German,
D.P. (2009) Do herbivorous minnows have "plug-flow reactor" guts?
Evidence from digestive enzyme activities, luminal nutrient
concentrations and gastrointestinal fermentation.
Journal of
Comparative Physiology B
179: 759-771
[pdf]
2006-08
Gao,
F., H. Yang, Q. Xu, F. Wang, G. Liu, and D.P. German (2008) Phenotypic
plasticity of gut structure and function during periods of inactivity
in
Apostichopus
japonicus
(Selenka).
Comparative
Biochemistry
and Physiology B 150: 255-262
[pdf]
German, D.P. and M.H. Horn (2006) Gut length and mass in herbivorous
and carnivorous prickleback fishes (Teleostei: Stichaeidae):
ontogenetic, dietary, and phylogenetic effects.
Marine Biology
148:
1123-1134
[pdf]
Horn, M.H., A. Gawlicka, D.P. German, E.A. Logothetis, J.W. Cavanagh
and K.S. Boyle (2006) Structure and function of the stomachless
digestive system in three related species of New World silverside
fishes (Atherinopsidae) representing herbivory, omnivory, and
carnivory.
Marine
Biology
149: 1237-1245
[pdf]
Pryor, G.S., D.P. German, and K.A. Bjorndal (2006) Gastrointestinal
fermentation in greater sirens (
Siren
lacertina).
Journal
of Herpetology 40: 112-117
[pdf]
Earlier
German, D.P., M.H. Horn and A. Gawlicka (2004) Digestive enzyme
activities in herbivorous and carnivorous prickleback fishes
(Teleostei: Stichaeidae): ontogenetic, dietary, and phylogenetic
effects.
Physiological
and
Biochemical Zoology 77(5):
789-804
[pdf]
Sturz, A., D.P. German and D. Putnam (1998). Salton Sea Geothermal
Area
Mud Pots: 1991-1998. In:
Geology and
Geothermal Resources of the
Imperial and Mexicali Valleys,
L. Lindsey and W. Hample (eds).
San
Diego Association of Geologists publication 98-1, Pg. 109-128.